U.S. patent application number 14/318339 was filed with the patent office on 2015-06-18 for systems and methods for producing stem cells and differentiated cells.
The applicant listed for this patent is NEW YORK STEM CELL FOUNDATION, INC.. Invention is credited to STEPHEN CHANG, KEVIN EGGAN, SCOTT NOGGLE, SUSAN SOLOMON.
Application Number | 20150166964 14/318339 |
Document ID | / |
Family ID | 53367680 |
Filed Date | 2015-06-18 |
United States Patent
Application |
20150166964 |
Kind Code |
A1 |
NOGGLE; SCOTT ; et
al. |
June 18, 2015 |
SYSTEMS AND METHODS FOR PRODUCING STEM CELLS AND DIFFERENTIATED
CELLS
Abstract
The present invention provides various improved systems and
methods for obtaining, generating, culturing, and handling cells,
such as stem cells (including induced pluripotent stem cells or
iPSCs) and differentiated cells, as well as cells and cell panels
produced using such systems and methods, and uses of such cells and
cell panels.
Inventors: |
NOGGLE; SCOTT; (LONG ISLAND
CITY, NY) ; EGGAN; KEVIN; (BOSTON, MA) ;
CHANG; STEPHEN; (POWAY, CA) ; SOLOMON; SUSAN;
(NEW YORK, NY) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
NEW YORK STEM CELL FOUNDATION, INC. |
NEW YORK |
NY |
US |
|
|
Family ID: |
53367680 |
Appl. No.: |
14/318339 |
Filed: |
June 27, 2014 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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13691258 |
Nov 30, 2012 |
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14318339 |
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61700792 |
Sep 13, 2012 |
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61580007 |
Dec 23, 2011 |
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61565818 |
Dec 1, 2011 |
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61840271 |
Jun 27, 2013 |
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Current U.S.
Class: |
435/366 ;
435/288.4; 435/377 |
Current CPC
Class: |
C12M 41/48 20130101;
C12M 23/12 20130101; C12M 41/46 20130101; C12M 47/04 20130101; C12N
5/0696 20130101 |
International
Class: |
C12N 5/074 20060101
C12N005/074; C12M 1/26 20060101 C12M001/26; C12M 1/32 20060101
C12M001/32; C12M 1/36 20060101 C12M001/36; C12M 1/34 20060101
C12M001/34 |
Claims
1. A method for the automated generation and/or manipulation of
stem cells, the method comprising: a) culturing multiple different
samples of cells, wherein the cells comprise adult somatic cells or
induced pluripotent stem cells, b) determining the proliferation
rate or cell doubling time of individual cell samples from among
the multiple different samples of cells, c) freezing individual
cell samples from among the multiple different samples of cells, d)
selecting from the individual cell samples a subset of samples
having similar proliferation rates or cell doubling times, e)
thawing the subset of samples selected in step (d), f) plating the
subset of samples in a multi-well plate, g) culturing the subset of
samples until they reach a desired confluency, and h) where the
cells comprise adult somatic cells, contacting the somatic cells
with one or more reprogramming factors in order to produce iPSCs,
or, where the cells comprise iPSCs, treating the iPSCs in order to
produce differentiated cells.
2. The method of claim 1, wherein the cells are derived from human
donors.
3. The method of claim 1, wherein the adult somatic cells are
fibroblasts.
4. The method of claim 1, wherein each of the steps is
automated.
5. The method of claim 1, wherein the individual cell samples in
the subset of samples have proliferation rates or cell doubling
times that are within 10% of one another.
6. The method of claim 1, wherein the culturing of step (g) is
performed in low serum medium.
7. The method of claim 1, wherein the step of selecting a subset of
samples further comprises selecting samples based the age, sex,
race, ethnicity, diagnosis, genotype, phenotype, blood type, HLA
type, treatment history, or drug response profile of the cell
sample or of the donor from which the cell sample was obtained.
8. The method of claim 1, wherein the step of treating the iPSCs in
order to produce differentiated cells comprises contacting the
iPSCs with one or more differentiation factors.
9. The method of claim 1, wherein the step of treating the iPSCs in
order to produce differentiated cells comprises generating embryoid
bodies (EBs).
10. The method of claim 9, wherein the step of generating embryoid
bodies (EBs) comprises plating iPSCs in V-bottom plates.
11. A automated system for grouping cells for parallel processing,
the system comprising: a) a component for determining the cell
proliferation rates or cell doubling times of multiple cell
samples, b) a component for cryopreserving the cell samples, c) a
component for selecting cell samples from among the multiple cell
samples having similar proliferation rates or cell doubling times,
d) a component for thawing the selected cell samples, and e) a
component for plating the selected samples in a multi-well
plate.
12. The automated system of claim 11, wherein the component for
determining the cell proliferation rates or cell doubling times
comprises a confluency checking unit.
13. The automated system of claim 11, further comprising an
induction unit which contacts the cells in the multi-well plate
with one or more reprogramming factors.
14. The automated system of claim 13, wherein the induction unit
contacts the cells in the multi-well plate with one or more
reprogramming factors after the cells have been cultured in low
serum medium for 5-7 days.
15. A method for the generation of induced pluripotent stem cells
(iPSCs) from adult somatic cells, the method comprising: a)
obtaining adult somatic cells, b) culturing the adult somatic cells
in low serum medium for more than 3 days, and c) subsequently
contacting the adult somatic cells with one or more reprogramming
factors, in order to produce iPSCs.
16. The method claim 15, wherein the population of adult somatic
cells obtained in step (a) had previously been frozen and were
thawed in low serum medium.
17. The method of claim 15, wherein the adult somatic cells are
human fibroblasts.
18. The method of claim 15, wherein the adult somatic cells are
cultured in low serum medium prior to contacting them with one or
more reprogramming factors.
19. The method of claim 18, wherein the adult somatic cells are
cultured in low serum medium for 5-7 days prior to contacting them
with one or more reprogramming factors.
20. The method of claim 18, wherein the low serum medium comprises
less than 3% serum.
Description
[0001] This application is a Continuation-In-Part application of
U.S. application Ser. No. 13/691,258, filed Nov. 30, 2012, now
pending, which claims benefit of priority under 35 U.S.C.
.sctn.119(e) of U.S. Provisional Patent Application No. 61/700,792,
filed Sep. 13, 2012; U.S. Provisional Patent Application No.
61/580,007, filed Dec. 23, 2011; U.S. Provisional Patent
Application No. 61/565,818, filed on Dec. 1, 2011; and which claims
benefit of priority under 35 U.S.C. .sctn.119(e) of U.S.
Provisional Patent Application No. 61/840,271 filed Jun. 27, 2013,
the entire contents of which are incorporated herein by reference
in their entireties.
[0002] A portion of the disclosure of this patent document contains
material that is subject to copyright protection. The copyright
owner has no objection to the facsimile reproduction by anyone of
the patent document or the patent disclosure as it appears in the
Patent and Trademark Office patent file or records, but otherwise
reserves all copyright rights whatsoever.
BACKGROUND OF THE INVENTION
[0003] Stem cells are unspecialized cells that self-renew for long
periods through cell division, and can be induced to differentiate
into cells with specialized functions, i.e., differentiated cells.
These qualities give stem cells great promise for use in
therapeutic applications to replace damaged cells and tissue in
various medical conditions. Embryonic stem (ES) cells are derived
from the blastocyst of an early stage embryo and have the potential
to develop into endoderm, ectoderm, and mesoderm (the three germ
layers) (i.e., they are "pluripotent"). In vitro, ES cells tend to
spontaneously differentiate into various types of tissues, and the
control of their direction of differentiation can be challenging.
There are unresolved ethical concerns that are associated with the
destruction of embryos in order to harvest human ES cells. These
problems limit their availability for research and therapeutic
applications.
[0004] Adult stem (AS) cells are found among differentiated
tissues. Stem cells obtained from adult tissues typically have the
potential to form a more limited spectrum of cells (i.e.,
"multipotent"), and typically only differentiate into the cell
types of the tissues in which they are found, though recent reports
have shown some plasticity in certain types of AS cells. They also
generally have a limited proliferation potential.
[0005] Induced pluripotent stem cells (iPSC or iPSCs) are produced
by laboratory methods from differentiated adult cells. iPSCs are
widely recognized as important tools, e.g., for conducting medical
research. Heretofore, the technology for producing iPSCs has been
time-consuming and labor-intensive. Differentiated adult cells,
e.g., fibroblasts, are reprogrammed, cultured, and allowed to form
individual colonies which represent unique clones. Previously,
identifying these types of cells has been difficult because the
majority of the cells are not fully-reprogrammed iPSC clones. The
standard is for iPSC clones to be selected based on the morphology
of the cells, with desirable colonies possessing sharply demarcated
borders containing cells with a high nuclear-to-cytoplasmic ratio.
When clones are identified, they are manually-picked by micro-thin
glass tools and cultured on "feeder" layers of cells typically,
murine embryonic fibroblasts (MEFs). This step is performed
typically at 14-21 days post-infection with a reprogramming vector.
Then the clones are expanded for another 14-21 days or more, prior
to undergoing molecular characterization.
[0006] Others have focused on developing techniques to rapidly and
more accurately identify and characterize fully-reprogrammed adult
fibroblasts and their downstream differentiation potential (Bock et
al., 2011, Cell 144: 439-452; Boulting et al., 2011, Nat Biotechnol
29: 279-286). Also see, for example, co-owned U.S. Ser. No.
13/159,030, filed on Jun. 13, 2011, describing the use of
Fluorescence Activated Cell Sorting (FACS) to identify and live
sort unique subpopulations of stem cells as defined by unique
expression patterns of surface proteins.
[0007] Thus, stem cells are an attractive source of cells for
therapeutic applications, medical research, pharmaceutical testing,
and the like. However, there remains a longstanding need in the art
for an automated system for rapidly producing and isolating
reproducible iPSC cell lines under standard conditions in order to
meet these and other needs. There also there remains in the art a
need for methods of making panels of iPSC cell lines, and
differentiated cells produced therefrom, that are derived from
multiple different individuals in a "population of interest."
SUMMARY OF THE INVENTION
[0008] The present invention provides various improved systems and
methods for obtaining, generating, culturing, and handling cells,
such as stem cells (including induced pluripotent stem cells or
iPSCs) and differentiated cells, as well as cells and cell panels
produced using such systems and methods, and uses of such cells and
cell panels. The present invention builds upon, and provides
certain improvements over, the systems and methods described
previously in international patent application PCT/US2012/067417
(published on Jun. 6, 2013 with publication number WO/2013/082509)
and U.S. patent application Ser. No. 13/691,258 (published on Dec.
26, 2013 with publication number 2013-0345094), the contents of
each of which are hereby incorporated by reference in their
entireties for those jurisdictions that permit incorporation by
reference. Building on the work described in these prior patent
applications, the Applicants have now developed certain improved
methods and systems that can significantly reduce variability in
obtaining, generating, culturing, and handling a variety of cell
types, including differentiated cells and stem cells. Such improved
systems and methods are particularly advantageous for automated
and/or high-throughput applications--greatly facilitating the
ability to work with large numbers of cells in a parallel
manner.
[0009] For example, the Applicants have discovered that variability
in the generation and culture and differentiated cells and stem
cells can be reduced, allowing for more efficient parallel
processing, if individual samples are selected and grouped
according to various characteristics (such as growth
characteristics or donor age), such that cells having similar
characteristics are grown and handled together. In some parts of
this application such methods may be referred to as "binning"
methods, or "batching" methods, or "binning and batching" methods,
or "data-driven batching" methods. Applicants also discovered that
the efficiency of cellular reprogramming could be improved, and the
variability in reprogramming efficiency reduced, when cells were
grown in low serum or serum free medium for a certain amount of
time prior to, and optionally also during, reprogramming. This
finding was unexpected given the widely-held view that growth rates
should be maximized for reprogramming. Indeed, consistent with this
prevailing view, cells are typically grown in high serum media
(e.g. containing 10% serum) prior to reprogramming and then
subsequently switched to low serum or serum free medium at a later
stage. While the Applicants, like others, found that increased
growth rates were beneficial for reprogramming, Applicants'
findings suggested that switching cells to low serum medium at the
time of, or soon after, reprogramming may shock the cells and have
a detrimental effect on reprogramming success. Applicants found
that such effects could be mitigated by allowing the cells to
adjust to low serum conditions for a certain amount of time prior
to reprogramming. Applicants also found that differences in methods
used to generate embryoid bodies (EBs) from pluripotent stem cells
had significant and surprising effects on differentiation. For
example, Applicants found that "hanging drop" methods for EB
generation led to a bias towards endoderm differentiation, while
the generation of EBs in V-bottom plates led to a more uniform
differentiation potential, as well we being better suited to
automated and high-throughput systems. These and other improvements
to systems and methods for obtaining, generating, culturing and
handling differentiated cells and stem cells, are described in
further detail in this Summary of the Invention section, as well as
throughout other sections of this patent application, including the
Detailed Description, Examples, Drawings & Claims.
[0010] As mentioned above, Applicants have discovered that
variability in the generation and culture of differentiated cells
and stem cells can be reduced if individual samples are selected
and grouped according to various characteristics, such that cells
having similar characteristics are grown and handled together. Such
methods can reduce variability in the generation and culture and
differentiated cells and stem cells, which is particularly
advantageous in applications requiring parallel processing of
multiple different samples, such as in automated and/or
high-throughput methods. Similarly, the ability to select, group
and handle samples according to various particular characteristics
may be useful for the generation of cell panels for use in a
variety of applications, including for use in drug screening. The
present invention provides a variety of methods and systems that
can be used to select and group samples in such ways. Such methods
and systems may be referred to herein as data-driven batching
methods or systems. Accordingly, in one embodiment the present
invention provides a method for the automated generation and/or
manipulation of stem cells, the method comprising: (a) culturing
multiple different samples of cells, wherein the cells comprise
adult somatic cells or induced pluripotent stem cells, (b)
determining the proliferation rate or cell doubling time of
individual cell samples from among the multiple different samples
of cells, (c) freezing individual cell samples from among the
multiple different samples of cells, (d) selecting from the
individual cell samples a subset of samples having similar
proliferation rates or cell doubling times, (e) thawing the subset
of samples selected in step (d), (f) plating the subset of samples
in a multi-well plate, (g) culturing the subset of samples until
they reach a desired confluency, and (h) where the cells comprise
adult somatic cells, contacting the somatic cells with one or more
reprogramming factors in order to produce iPSCs, or, where the
cells comprise iPSCs, treating the iPSCs in order to produce
differentiated cells. Similarly, in one embodiment the present
invention provides a method for the efficient generation, culture
and/or handling of multiple cell samples in parallel, the method
comprising: (a) culturing multiple different cell samples, (b)
determining, or obtaining information regarding, one or more
characteristics or properties of individual samples from among the
multiple different cell samples (or of the donor/subject from which
such samples were obtained), (c) selecting from the multiple
different cell samples a subset of cell samples having a desired
characteristic or property, (d) plating the subset of cell samples
in a multi-well plate, and (e) culturing the subset of cell samples
in the multi-well plate. Similarly, in other embodiment, the
present invention provides a method for the efficient culture of
multiple cell samples in parallel, the method comprising: (a)
culturing multiple different cell samples, (b) determining, or
obtaining information regarding, one or more characteristics or
properties of individual samples from among the multiple different
cell samples (or of the donor/subject from which such samples were
obtained), (c) freezing individual cell samples from among the
multiple different cell samples, (d) selecting from the multiple
different cell samples a subset of cell samples having a desired
characteristic or property, (e) thawing the subset of cell samples
selected in step (d) plating the subset of cell samples in a
multi-well plate, and (f) culturing the subset of cell samples in
the multi-well plate. In some such embodiments the characteristic
or property is the cellular proliferation rate or cell doubling
time of a cell sample. In some such embodiments, the characteristic
or property relates to the age, sex, race, ethnicity, diagnosis
(e.g. for a disease or a disorder), genotype, phenotype, blood
type, HLA type, treatment history, or drug response profile of the
cell sample or of the donor/subject from which the cell sample was
obtained. In some such embodiments cell samples are selected on the
basis of at least two characteristics, including (i) the cellular
proliferation rate or cell doubling time of the cell sample, and
(ii) the age, sex, race, ethnicity, diagnosis (e.g. for a disease
or a disorder), genotype, phenotype, blood type, HLA type,
treatment history, or drug response profile of the cell sample or
the donor/subject from which the cell sample was obtained. In some
such embodiments the cell samples are adult somatic cells, such as
adult somatic fibroblasts. In some such embodiments the cell
samples are pluripotent stem cells, such as induced pluripotent
stem cell (iPSCs). In some such embodiments the cell samples are
differentiated cells derived from pluripotent stem cells. In some
such embodiments one or more of the steps is automated. In some
embodiments, each of the steps is automated. In some such
embodiments the step of selecting from the multiple different cell
samples a subset of the cell samples is automated and/or performed
by a computer. In some such embodiments, where samples are selected
based on having similar proliferation rates or cell doubling times,
the selected samples have proliferation rates or cell doubling
times that vary by less than 30% between samples, or by less than
25% between samples, or by less than 20% between samples, or by
less than 15% between samples, or by less than 10% between samples,
or by less than 5% between samples, or by less than 2% between
samples.
[0011] In another embodiment, the present invention provides a
method for the efficient generation of induced pluripotent stem
cells from differentiated adult somatic cells, the method
comprising: (a) culturing multiple different samples of
differentiated adult somatic cells, (b) determining the
proliferation rate or cell doubling time of individual samples from
among the multiple different samples of differentiated adult
somatic cells, (c) selecting from the multiple different samples of
differentiated adult somatic cells a subset of samples having
similar proliferation rates or cell doubling times, (d) plating the
subset of the samples selected in a multi-well plate, such that
each of the samples in the multi-well plate has a similar
proliferation rate or cell doubling time, (e) culturing the cell
samples in the multi-well plate until they reach a desired
confluency, and (f) contacting the cell samples with one or more
reprogramming factors in order to produce iPSCs. Similarly, in
another embodiment, the present invention provides a method for the
automated generation of induced pluripotent stem cells from
differentiated adult somatic cells, the method comprising: (a)
culturing multiple different samples of differentiated adult
somatic cells, (b) determining the proliferation rate or cell
doubling time of individual samples from among the multiple
different samples of differentiated adult somatic cells, (c)
freezing individual cell samples from among the multiple different
cell samples, (d) selecting from the multiple different samples of
differentiated adult somatic cells a subset of the samples having
similar proliferation rates or cell doubling times, (e) thawing and
plating the subset of the samples selected in step (d) into a
multi-well plate, such that each of the samples in the multi-well
plate has a similar proliferation rate or cell doubling time, (f)
culturing the cell samples in the multi-well plate until they reach
a desired confluency, and (g) contacting the cell samples with one
or more reprogramming factors in order to produce iPSCs. In some
such embodiments the differentiated adult somatic cells are
fibroblasts. In some such embodiments the fibroblasts are derived
from human donors/subjects. In some such embodiments one or more of
the steps is automated. In some such embodiments, each of the steps
is automated. In some such embodiments the step of selecting from
the multiple different cell samples a subset of the cell samples
having similar proliferation rates or cell doubling times is
performed by a computer. In some such embodiments, where samples
are selected based on having similar proliferation rates or cell
doubling times, the selected samples have proliferation rates or
cell doubling times that vary by less than 30% between samples, or
by less than 25% between samples, or by less than 20% between
samples, or by less than 15% between samples, or by less than 10%
between samples, or by less than 5% between samples, or by less
than 2% between samples. In some such embodiments the culturing of
the somatic cells prior to contacting with reprogramming factors is
performed in low serum medium or in serum free medium. In some such
embodiments the step of selecting a subset of the cell samples
further comprises selecting cell samples on the basis of the age,
sex, race, ethnicity, diagnosis (e.g. for a disease or a disorder),
genotype, phenotype, blood type, HLA type, treatment history, or
drug response profile of the cell sample or the donor/subject from
which the cell sample was obtained. In some such embodiments the
method further comprises producing differentiated cells from the
pluripotent stem cells, for example by contacting the pluripotent
stem cells with one or more differentiation factors or by
generating embryoid bodies (EBs). In some such embodiments, where
EBs are generated from pluripotent stem cells, the EBs are
generated in V-bottom plates.
[0012] In one embodiment, the present invention provides a method
for the efficient generation of human induced pluripotent stem
cells (iPSCs) from human donor fibroblasts, the method comprising:
(a) culturing multiple different samples of human donor
fibroblasts, (b) determining the proliferation rate or cell
doubling time of individual samples from among the multiple
different samples of human donor fibroblasts, (c) freezing
individual cell samples from among the multiple different samples
of human donor fibroblasts, (d) selecting from the multiple
different samples of human donor fibroblasts a subset of the
samples having similar proliferation rates or cell doubling times,
(e) thawing the subset of samples selected in step (d), (f)
culturing the subset of cell samples in a multi-well plate, such
that each of the samples in the multi-well plate has a similar
proliferation rate or cell doubling time, wherein the culturing
comprises contacting the cell samples with low serum medium for at
least 3 days, and (g) subsequently contacting the cell samples with
one or more reprogramming factors in order to produce iPSCs. In one
such embodiment one or more of the steps is automated. In one such
embodiment each of the steps is automated. In one such embodiment
the step of selecting from the multiple different cell samples a
subset of the cell samples having similar proliferation rates or
cell doubling times is automated and/or performed by a computer. In
some such embodiments, where samples are selected based on having
similar proliferation rates or cell doubling times, the selected
samples have proliferation rates or cell doubling times that vary
by less than 30% between samples, or by less than 25% between
samples, or by less than 20% between samples, or by less than 15%
between samples, or by less than 10% between samples, or by less
than 5% between samples, or by less than 2% between samples. In one
such embodiments the step of selecting a subset of the cell samples
further comprises selecting cell samples on the basis of the age,
sex, race, ethnicity, diagnosis (e.g. for a disease or a disorder),
genotype, phenotype, blood type, HLA type, treatment history, or
drug response profile of the cell sample or the donor/subject from
which the cell sample was obtained.
[0013] In one embodiment, the present invention provides a method
for the automated generation of differentiated cells from
pluripotent stem cells, the method comprising: (a) culturing
multiple different samples of pluripotent stem cells, (b)
determining the proliferation rate or cell doubling time for
individual samples from among the multiple different samples of
pluripotent stem cells, (c) selecting from the multiple different
samples of pluripotent stem cells a subset of samples having
similar proliferation rates or cell doubling times, (d) plating the
subset of the samples selected in step (c) into a multi-well plate,
such that each of the samples in the multi-well plate has a similar
proliferation rate or cell doubling time, (e) culturing the cell
samples in the multi-well plate until they reach a desired passage
number and/or confluency, and (f) producing differentiated cells
from the pluripotent stem cells. Similarly, in another embodiment,
the present invention provides a method for the automated
generation of differentiated cells from pluripotent stem cells, the
method comprising: (a) culturing multiple different samples of
pluripotent stem cells, (b) determining the proliferation rate or
cell doubling time for each of the multiple different samples of
pluripotent stem cells, (c) freezing individual cell samples from
among the multiple different cell samples, (d) selecting from the
multiple different samples of pluripotent stem cells a subset of
the samples having similar proliferation rates or cell doubling
times, (e) thawing and plating the subset of the samples selected
in step (x) into a multi-well plate, such that each of the samples
in the multi-well plate has a similar proliferation rate or cell
doubling time, (f) culturing the cell samples in the multi-well
plate until they reach a desired passage number and/or confluency,
and (g) producing differentiated cells from the pluripotent stem
cells. In some such embodiments the pluripotent stem cells are
induced the pluripotent stem cells (iPSCs). In some such
embodiments one or more of the steps is automated. In some such
embodiments the each of the steps is automated. In some such
embodiments the step of selecting from the multiple different cell
samples a subset of the cell samples having similar proliferation
rates or cell doubling times is automated and/or performed by a
computer. In some such embodiments, where samples are selected
based on having similar proliferation rates or cell doubling times,
the selected samples have proliferation rates or cell doubling
times that vary by less than 30% between samples, or by less than
25% between samples, or by less than 20% between samples, or by
less than 15% between samples, or by less than 10% between samples,
or by less than 5% between samples, or by less than 2% between
samples. In some such embodiments, the step of producing
differentiated cells from the iPSCs comprises contacting the iPSCs
with one or more differentiation factor. In some such embodiments
the step of producing differentiated cells from the iPSCs comprises
generating embryoid bodies (EBs). In some such embodiments the step
of producing differentiated cells from the iPSCs comprises
generating embryoid bodies (EBs) in V-bottom plates. In some such
embodiments the step of selecting a subset of the cell samples
further comprises selecting cell samples on the basis of the age,
sex, race, ethnicity, diagnosis (e.g. for a disease or a disorder),
genotype, phenotype, blood type, HLA type, treatment history, or
drug response profile of the cell sample or the donor/subject from
which the cell sample was obtained.
[0014] The present invention also provides automated "data-driven
batching systems" that can be used to select and group (or "bin
and/or batch") cell samples based on one or more properties or
characteristics, as described above. Such automated data-driven
batching systems systems can be used, for example, to select and
group somatic cells (such as fibroblasts) for analysis or for
subsequent iPSC generation, to select and group stem cells (such as
iPSCs) for analysis or for subsequent differentiation, and/or to
select and group cells (such as somatic cells obtained from donors,
iPSCs, or differentiated cells derived from iPSCs) for inclusion in
a cell panel. The components of the data-driven batching systems
described here can comprise, or can be modified from, or can be
used in conjunction with, the other automated systems, and
components thereof, described herein and/or those described in
international patent application PCT/US2012/067417 and U.S. patent
application Ser. No. 13/691,258. Further, one of skill in the art
will appreciate where and how the automated systems described
herein (and in PCT/US2012/067417 and U.S. Ser. No. 13/691,258) can
be modified to provide or include such data-driven batching
systems.
[0015] For example, in some embodiments, the present invention
provides an automated data-driven batching system that comprises:
(a) a component/system for determining the cell proliferation rate
or cell doubling time of a cell sample, (b) a component/system for
selecting and/or retrieving cell samples having a desired cell
proliferation rate or cell doubling time, and (c) a
component/system for plating the selected samples in a multi-well
plate. Similarly, in some embodiments, the present invention
provides an automated data-driven batching system that comprises:
(a) a component/system for determining the cell proliferation rate
or cell doubling time of a cell sample, (b) a component/system for
cryopreserving a cell sample, (c) a component/system for selecting
and/or retrieving cryopreserved cell samples having a desired cell
proliferation rate or cell doubling time, (d) a component/system
for thawing the selected cryopreserved cell samples, and (e) a
component/system for plating the selected samples in a multi-well
plate. In some such embodiments, the component/system of the
data-driven batching system used to determine the cell
proliferation rate or cell doubling time of a cell sample may
comprise an automated cell imager (such as a Celigo imager) or
other automated device that can be used to measure cell confluency
or cell numbers, or some other parameter from which cell
proliferation rate or cell doubling time can be calculated (such as
a confluency checking unit). In some such embodiments, the
component/system for cryopreserving the cell sample may comprise a
system for robotically transferring cell samples into
cryopreservation tubes (such as barcoded cryopreservation tubes)
and may comprise a 80.degree. C. freezer. In some such embodiments,
the component/system for selecting cell samples having a desired
cell proliferation rate or cell doubling time may comprise a
computer system programmed with desired selection criteria, and/or
may comprise an automated sample access system, such as a
-80.degree. C. Sample Access Manager or "SAM" (Hamilton Storage
Technologies). Such an automated sample access system may comprise
an inventory database that allows for flexible recall and
downstream process batching of cell samples, for example based on
one or more factors such as cell proliferation rate, cell doubling
time, or any other desired property or characteristic.
[0016] In some embodiments such data-driven batching systems form
part of a larger automated system, such as the larger automated
systems described herein for the generation of iPSCs and/or
differentiated cells. For example, in one embodiment the present
invention provides an automated system for generating and isolating
iPSCs, comprising: (a) a somatic cell plating unit for placing
somatic cells on a plate; (b) a data-driven batching system used to
select somatic cell samples for reprogramming, and (c) an induction
unit for automated reprogramming of the somatic cells by contacting
the somatic cells on the somatic cell plating unit with
reprogramming factors to produce iPSCs. In one such embodiment, the
system further comprises a sorting unit for selectively sorting and
isolating the iPSCs produced by the induction unit, e.g., by
identifying iPSC specific markers, including, e.g., surface markers
on the cells. In one illustrative example, the somatic cells are
fibroblasts. Similarly, in another embodiment the present invention
provides an automated system for generating and isolating
differentiated adult cells from stem cells, e.g., iPSCs, embryonic
stem (ES) cells or mesenchymal stem (MS) cells, comprising: (a) a
stem cell plating unit for placing stem cells on a plate; (b) a
data-driven batching system used to select stem cell samples for
subsequent differentiation and (c) an induction unit for automated
differentiation of stem cells, for example by contacting the cells
on the with one or more differentiation factors to produce
differentiated cells. In one such embodiment, the system further
comprises a sorting unit for selectively sorting and isolating the
differentiated cells produced by the induction unit.
[0017] As described above, it is a discovery of the present
invention that the efficiency of cellular reprogramming can be
improved, and variability in reprogramming efficiency reduced, when
cells are grown in low serum or serum free medium for a certain
amount of time prior to, and optionally also during, contacting
cells with reprogramming factors. While the Applicants, like
others, found that increased growth rates were beneficial for
reprogramming, Applicants' findings suggested that switching cells
to low serum medium at the time of, or soon after, reprogramming
may shock the cells and have a detrimental effect on reprogramming
success. Applicants found that such effects could be mitigated by
allowing the cells to adjust to low serum conditions for a certain
amount of time prior to reprogramming. Accordingly, in one
embodiment the present invention provides a method for the
generation of induced pluripotent stem cells (iPSCs) from
differentiated adult somatic cells, the method comprising: (a)
obtaining adult somatic cells, (b) culturing the adult somatic
cells in low serum medium days, and (c) subsequently contacting the
adult somatic cells with one or more reprogramming factors, in
order to produce iPSCs. In some such embodiments the population of
adult somatic cells obtained in step (a) had previously been
frozen. In some such embodiments the population of adult somatic
cells had been thawed in low serum medium. In some such embodiments
the adult somatic cells are fibroblasts. In some such embodiments
the adult somatic cells are cultured in low serum medium for more
than 1 day prior to contacting the adult somatic cells with one or
more reprogramming factors. In some such embodiments the adult
somatic cells are cultured in low serum medium for more than 2 days
prior to contacting the adult somatic cells with one or more
reprogramming factors. In some such embodiments the adult somatic
cells are cultured in low serum medium for more than 3 days prior
to contacting the adult somatic cells with one or more
reprogramming factors. In some such embodiments the adult somatic
cells are cultured in low serum medium for more than 4 days prior
to contacting the adult somatic cells with one or more
reprogramming factors. In some such embodiments the adult somatic
cells are cultured in low serum medium for more than 5 days prior
to contacting the adult somatic cells with one or more
reprogramming factors. In some such embodiments the adult somatic
cells are cultured in low serum medium for more than 6 days prior
to contacting the adult somatic cells with one or more
reprogramming factors. In some such embodiments the adult somatic
cells are cultured in low serum medium for more than 7 days prior
to contacting the adult somatic cells with one or more
reprogramming factors. In some such embodiments the adult somatic
cells are cultured in low serum medium for 5-7 days prior to
contacting the adult somatic cells with one or more reprogramming
factors. In some such embodiments the adult somatic cells are
cultured in low serum medium for 4-8 days prior to contacting the
adult somatic cells with one or more reprogramming factors. In some
such embodiments the adult somatic cells are cultured in low serum
medium for 3-9 days prior to contacting the adult somatic cells
with one or more reprogramming factors. In some such embodiments
the adult somatic cells are cultured in low serum medium for 2-10
days prior to contacting the adult somatic cells with one or more
reprogramming factors. In some such embodiments the step of
contacting the adult somatic cells with one or more reprogramming
factors is performed while the adult somatic cells are in low serum
medium. In some such embodiments the low serum medium comprises
less than 5% serum. In some such embodiments the low serum medium
comprises less than 4% serum. In some such embodiments the low
serum medium comprises less than 3% serum. In some such embodiments
the low serum medium comprises less than 2% serum. In some such
embodiments the low serum medium comprises less than 1% serum. In
some such embodiments the low serum medium is serum free. In some
such embodiments the low serum medium comprises a serum
replacement. Several different serum replacements are known in the
art and any such serum replacement can be used.
[0018] In certain embodiments the present invention also provides
cells, such as somatic cells (e.g. donor-derived fibroblasts),
pluripotent stem cells (such as iPSCs), differentiated cells
produced from pluripotent stem cells (such as hematopoetic cells,
muscle cells, cardiac muscle cells, liver cells, cartilage cells,
epithelial cells, urinary tract cells, and neuronal cells), and
transdifferentiated cells, such as those produced using the methods
and systems described herein. The present invention also provides
"arrays" or "panels" or "banks" comprising such cells. In some
embodiments such cell arrays, panels or banks may comprise cells
derived from multiple different individuals, for example multiple
different individuals in a "population of interest." The population
of interest can be any population desired, including, but not
limited to, the world population, the population of a particular
country, the population of a particular continent, the population
of a particular geographic region, the population of a particular
racial or ethnic group, a population of a particular age, a
population of a particular sex (male or female), a population
having a particular disease or disorder, a population having a
particular mutation, a population having a particular genotype, a
population having a particular phenotype, a population having a
particular blood type, a population having a particular HLA type, a
population having a particular drug response profile, and the like.
In some embodiments the individuals from whom cells are derived are
selected in order to be representative of the variation in the
particular population of interest. For example, if the population
of interest is the U.S. population, the individuals from whom cells
are derived are preferably selected to be representative of the
U.S. population (e.g. in terms of race/ethnicity and/or any other
desired characteristic), for example based on census data or some
other suitable criteria. In some embodiments the cell panels
comprise isogenic control cells. For example, in embodiments where
the cell panels contain cells having a certain mutation, the panels
may comprise control cells in which that mutation is not present
(for example if it has been corrected) but where the cells are
otherwise genetically identical. In some embodiments the cells in
the cell panels comprise a reporter gene, such as a reporter gene
that can be used to report expression of a gene or gene product
that is or may be involved in a disease, or is in a pathway that is
or may be involved in a disease. In some embodiments the cell
panels comprise both sporadic and familial lines. For example, in
the case of a panel containing samples from subjects having a
certain disease, the panel may comprise samples from subjects in
which that disease arose as the result of a sporadic mutation, as
well as samples from subjects in which that disease was inherited.
In some embodiments, the cell panels comprise 3 or more cell
lines/clones from each subject, in order to provide replicates of
samples from each subject. In some embodiments the present
invention provides populations of stem cells (such as iPSCs) or
differentiated cells wherein the populations of cells are derived
from at least 96, or at least 384, or at least 1596 different
individuals from the population of interest. In preferred
embodiments cells from different individuals are provided in
separate vessels, such as separate wells of a 96-well, 384-well, or
1596-well microtiter plate.
[0019] The cells, arrays, panels and banks of the invention may be
useful in a variety of different applications, for example in
studying or determining the efficacy, toxicity, teratogenicity or
safety of, one or more candidate drugs on cells of different
individuals in a population of interest. As such the cell panels of
the invention can be used to perform "clinical trials in a
dish."
[0020] In some embodiments the present invention also provides gene
sets and probe sets that may be useful for detection of iPSCs or
differentiated cells, such as those made using the automated
systems of the present invention. Such gene and probe sets can be
used in as part of one of the automated systems of the invention or
in other applications, as desired.
[0021] In one embodiment the present invention provides a "Pluri25"
gene/probe set comprising the following genes, or probes for
detecting expression of the following genes: retroviral tOct4,
retroviral tSox2, retroviral tKlf4, retroviral tC-Myc, Sendai
tOct4, Sendai tSox2, Sendai tKlf4, Sendai tC-Myc, Sendai vector
(SeV), POU5F1 (Oct4), SOX2, KLF4, MYC, LIN28, NANOG, ZFP42, SOX17,
AFP, NR2F2, ANPEP (CD13), ACTB, POLR2A, ALAS1, SRY and XIST.
[0022] In another embodiment the present invention provides a
gene/probe set for detection of iPSCs comprising the following
genes, or probes for detecting expression of the following genes:
Sendai tOct4, Sendai tSox2, Sendai tKlf4, Sendai tC-Myc, Sendai
vector (SeV), POU5F1 (Oct4), SOX2, KLF4, MYC, LIN28, NANOG, ZFP42,
SOX17, AFP, NR2F2, ANPEP (CD13), ACTB, POLR2A, ALAS1, SRY and
XIST.
[0023] In another embodiment the present invention provides a
gene/probe set for detection of iPSCs comprising the following
genes, or probes for detecting expression of the following genes:
retroviral tOct4, retroviral tSox2, retroviral tKlf4, retroviral
tC-Myc, POU5F1 (Oct4), SOX2, KLF4, MYC, LIN28, NANOG, ZFP42, SOX17,
AFP, NR2F2, ANPEP (CD13), ACTB, POLR2A, ALAS1, SRY and XIST.
[0024] In another embodiment the present invention provides a
gene/probe set for detection of iPSCs comprising the following
genes, or probes for detecting expression of the following genes:
POU5F1 (Oct4), SOX2, KLF4, MYC, LIN28, NANOG, ZFP42, SOX17, AFP,
NR2F2, ANPEP (CD13), ACTB, POLR2A, ALAS1, SRY and XIST.
[0025] In another embodiment the present invention provides a
gene/probe set referred to as the "3GLSC100" gene/probe set, which
is useful for detection of iPSCs and which comprises the genes, or
probes for detecting expression of the genes, listed in Table 2 in
the Detailed Description section of the present application.
[0026] In some embodiments the present invention also provides
gene/probe sets for detection of cells that have begun to
differentiate into cardiomyocytes. One such gene/probe set,
referred to as the "cardiac 1" gene/probe set, comprises the
following genes, or probes for detecting expression of the
following genes: ACTN1, BMP4, GATA4, GJA1, IRX-4, ISL1, KDR, MEF2A,
MEF2C, MESP1, MYH6, MYH7, MYL2, MYL7, NKX2-5, NPPA, PDGFRa, SIRPA,
TBX20, TBX5, TNNI3, TNNT2, VCAM1, VWF, MIXL1, NANOG, OCT4, SOX17,
Brachury T and KCNJ2. Another such gene/probe set, referred to as
the "cardiac 2" gene/probe set, comprises the following genes, or
probes for detecting expression of the following genes: ACTN1,
BMP4, GATA4, GJA1, IRX-4, ISL1, KDR, MEF2A, MEF2C, MESP1, MYH6,
MYH7, MYL2, MYL7, NKX2-5, NPPA, PDGFRa, SIRPA, TBX20, TBX5, TNNI3,
TNNT2, VCAM1, VWF, MIXL1, NANOG, OCT4, SOX17, Brachury T, KCNJ2,
GAPDH, GUSB, HPRT1, and TBP.
[0027] In another embodiment the present invention provides methods
for obtaining reprogrammed human fibroblasts from mixed cell
populations (for example using the automated methods described
herein) by isolating cells that are CD13-negative, SSEA4-positive
and Tra-1-60-positive, wherein the CD13-negative, SSEA4-positive
and Tra-1-60-positive cells are reprogrammed human fibroblasts. In
some embodiments such methods utilize fluorescence activated cell
sorting (FACS).
BRIEF DESCRIPTION OF THE DRAWINGS
[0028] FIG. 1. Steps for acquiring a fibroblast cell bank.
[0029] FIG. 2. Steps for obtaining a stem cell array from a
fibroblast bank.
[0030] FIG. 3. Flowchart showing steps in a system for producing
iPSCs.
[0031] FIGS. 4A-4C. Examples of a flow of patient samples through
multi-well tissue culture plates during an automated reprogramming
process.
[0032] FIGS. 5A-5C. Example of an equipment configuration to
accomplish the workflow.
[0033] FIGS. 6A-6C. Automated biopsy outgrowth tracking system. In
FIG. 6A, biopsies or discarded tissue are plated in multiple wells
of a 6-well dish and maintained by an automated system that feeds,
images, passages, and freezes fibroblast outgrowths. Examples of
the image analysis interface are shown for a typical sample. FIG.
6B: Cell numbers are extrapolated from confluence measurements
based on linear regression from a standard curve generated
independently. FIG. 6C: An example of cell counts for a typical
biopsy outgrowth maintained on an automated system provided by the
invention. Extrapolated cell numbers per patient sample are plotted
for each well independently (top) allowing calculation of total
output from the sample (bottom).
[0034] FIGS. 7A-D. FACS analyses and graphs showing automated iPSC
reprogramming. Expression levels of pluripotent surface markers on
reprogrammed human fibroblasts were followed over a 3 week period
to observe reprogramming kinetics and determine optimal time points
at which to isolate defined cell populations. FIG. 7A FACS gating
scheme used for analysis. FIG. 7B: A substantial proportion of
cells co-expressing traditional pluripotency surface markers SSEA4
& TRA-1-60 retain the fibroblast marker CD13 at all time points
during reprogramming using viral vectors to introduce reprogramming
factors such as Oct4, Sox2, Klf4 and c-Myc. Box plots indicating
aggregated data from 131 experiments (Retrovirus, n=66, Sendai
virus, n=65) are shown. While Sendai mediated reprogramming
produces more SSEA4/TRA-1-60 double positive cells, (C) there is a
delay in elimination of CD13 from the surface. (D) Example staining
pattern of a patient cell line reprogrammed using Sendai/Cytotune
system on an automated system provided by the invention. At both 7
and 13 days post infection (dpi), more than half of SSEA4/TRA-1-60
double positive cells have lost CD13. Additionally, at both time
points assayed, CD13 negative/Nanog positive cells are present in
this fraction, suggesting these can be isolated by negative
selection against CD13.
[0035] FIGS. 8A-C. FACs pre-sort analyses and a part of the
automated system to demonstrate enrichment and clone selection of
iPSCs. FIG. 8A shows Non-reprogrammed cell populations can be
depleted from cultures of iPSCs by negative selection by a
fibroblast marker. In the example, fibroblasts are efficiently
removed from the culture containing 2% established iPSCs leaving
TRA-1-60 positive iPSCs untouched. FIG. 8B shows a Miltenyi
MultiMACS system integrated into Hamilton liquid handler that can
sort 24 samples in parallel. FIG. 8C is an illustration of the
iPSC-enriched fraction from the anti-fibroblast magnetic negative
selection step that is plated on 96-well imaging plates at limiting
dilution. These plates are screened using live-cell staining for
the pluripotency surface marker TRA-1-60 or TRA-1-81. Wells with
TRA-1-60 positive iPSCs are identified by automated image analysis
using the Celigo software capable of single colony confirmation.
Wells that meet both criteria of containing a single colony that is
positive for the surface marker are selected for passaging,
expansion, and QC.
[0036] FIGS. 9A-B. Illustration for the scorecard assays described
herein. The first stage of the quality control screen uses a panel
of pluripotency differentiation and transgene markers to choose an
initial set of three clones. (A) Transcript counts after
normalization to HK gene expression for two human ESC lines, Sendai
positive control, fibroblast negative control, and iPSC lines
derived by FACS sorting assayed at passage 5 and 10. All assays are
run relative to a panel of normal human ESC and iPSC lines
maintained under similar conditions. (B) Second stage of a quality
control screen, which uses an additional 83 germ layer/lineage
markers to monitor differentiation capability in embryoid body
assays. Single EBs are generated and pooled to collect RNA for
expression analysis of germ layer markers in the embryoid body
scorecard assay. Shown is a cluster dendrogram analysis of gene
expression in EBs collected from nine different embryonic stem
cells lines. After normalization, data generated from direct lysis
of six EBs compares favorably to data generated from total RNA
extracted and purified from EBs prepared from bulk culture.
[0037] FIGS. 10A-B. High throughput karyotyping of iPSCs based on
Nanostring nCounter assays for CNVs. (A) is an example of the
nCounter Karyotype assay on BC1 iPSCs; (B) is an example of the
nCounter Karyotype assay on 1016 fibroblasts with partial gain and
loss of chromosome arms. Comparison to Affymetrix SNP 6.0 chip data
demonstrating copy number gains on a portion of the q arm of Chr1
(top track, 1q21.2-1q43) and loss of part of the long arm of Chr6
(bottom track, 6q16.3-6q26).
[0038] FIGS. 11A-E. Enhanced derivation and maintenance of virally
reprogrammed fibroblasts using Fluorescence Activated Cell Sorting.
(A) CD13NEGSSEA4POSTra-1-60NEG and CD13NEGSSEA4POSTra-1-60POS
populations from the manually derived 1018 clone were sorted onto
MEF feeder layers and expanded for 20 days prior to reanalysis by
flow cytometry to assess retention of sorted surface markers.
dpi=days post infection. dps=days post sort. (B) CD13NEGSSEA4POS
and CD13NEGSSEA4POSTra-1-60POS populations were sorted onto MEF
layers at seven days post infection and imaged at 3 and 17 dps to
assess colony formation. (C) Colony counts arising from the sorted
cell populations shown in Panel B at 17 dps (25 dpi). (D) Gating
structure used in the analysis of CD13POS cells present within the
SSEA4POSTra-1-60POS population at 7 dpi. (E) Fluorescence
microscopy demonstrating NANOG expression in CD13POS cell at 7 dpi.
40.times. magnification. CD13 shown in red. Nanog in shown Green.
Values designated % T indicates proportion of total cells within
the culture positive for the indicated combinations of surface
markers. Values without T designation indicate the proportion of
CD13NEGSSEA4POS cells that are Tra-1-60POS or Tra-1-60NEG in Panel
A and D.
[0039] FIGS. 12A-D. Fibroblasts undergoing viral reprogramming
exhibit characteristic expression levels of surface markers at
early time points post infection. (A) Foreskin (0825) and adult
dermal fibroblast (1018 and 1023) lines underwent four factor
retroviral reprogramming and were analyzed by flow cytometry for
the emergence of the CD13.sup.NEGSSEA4.sup.POSTra-1-60.sup.POS
population at seven day intervals post infection. Values designated
% T indicates proportion of total cells within the culture positive
for the indicated combinations of surface markers. Values without T
designation indicate the proportion of cells positive within the
parent gate. (B) Gating structure used to sort the
CD13.sup.NEGSSEA4.sup.POSTra-1-60.sup.POS populations for all cell
lines derived in this study. Live cell are first defined using
forward (FSC) and Side (SSC) light scattering properties. The
CD13.sup.NEGSSEA4.sup.POS population is then selected from the live
cell gate (blue cells). The highest Tra-1-60.sup.POS expressing
cells are then selected from the CD13.sup.NEGSSEA4.sup.POS
population (Green cells) and sorted for expansion and
characterization. (C) Comparison of SSEA4.sup.POSTra-1-60.sup.POS
populations present in Retro (R) or Sendai (S) viral infected
fibroblast cultures during first two weeks of programming. (D)
Comparison of CD13.sup.POS cells present within the
SSEA4.sup.POSTra-1-60.sup.POS populations during first two weeks of
programming following Retro (R) or Sendai (S) infection. Dpi
1-7:(R) n=29, (S) n=21. Dpi 8-14: (R) n=32, (S) n=46. Total n=228.
Statistical significance was assessed via Student's t-Test.
*p<=0.05, **p<=0.001, ***p<=0.001, ****p<=0.0001.
[0040] FIGS. 13A-C. Fluorescence Activated Cell Sorting generates
higher quality independent clones than manual derivation. Modified
pluripotent scorecard assay was performed on manually and FACS
derived clones to demonstrate (A) activation of endogenous gene
expression and (B) silencing of gene expression and presence of
unreprogrammed and transformed fibroblasts CD13.sup.POS in manually
derived clones. (C) Three sorted and three picked lines from
patient 1023 were used to compare the ability of both methods to
generate independent clones. 10.mu. of genomic DNA were cut
overnight with BglII and submitted to Southern blotting. The HUES
line HES2 was used as a positive control for endogenous KLF4/OCT4,
and as a negative control for transgene insertions. Samples were
first blotted for KLF4, then stripped and reblotted for OCT4.
Picked clones 1023 C and E are consistent with being the same clone
by both KLF4 and OCT4 blotting. * indicated the predicted
endogenous KLF4/OCT4 bands, and ** indicated a consistent band
found in all samples blotted with OCT4.
[0041] FIGS. 14A-E. hIPSC lines derived by Fluorescence Activated
Cell Sorting possess in vitro and in vivo spontaneous differential
potential. Embryoid bodies were derived from FACS (A) or manually
derived clones (B) and stained for expression of alpha fetoprotein,
smooth muscle actin and beta III tubulin (Tuj1) to demonstrate
differentiation potential in vitro potential. 10.times.
Magnification (C) Differentiation potential of the derived lines
for expression of germ layer genes present in the Lineage scorecard
assay. (D) Teratomas from FACS (D) or manually derived (E) clones
of 1023 fibroblast line indicating in vitro differentiation
potential by formation of three germ layers.
[0042] FIGS. 15A-B. Stability of Fluorescence Activated Cell Sorted
and Manually Derived IPSC Lines. Three individual clones were
selected from foreskin (0819) fibroblasts lines which previously
underwent four factor retroviral reprogramming and were derived by
either FACS (A, C.sub.1-C.sub.3) or manual (B, C.sub.4-C.sub.6)
techniques were analyzed by flow cytometry for pluripotent surface
marker expression following expansion on murine embryonic
fibroblasts for 12-14 passages. Clones C3 and C6 were adapted to
Matrigel and mTSER media around passage11 and expanded for several
passages prior to surface marker analysis by flow cytometry to
demonstrate stability following changes in culture conditions.
Events displayed in the 2D scatter plots are "live" cells as
defined by forward and side scatter properties expressing indicated
surface markers.
[0043] FIGS. 16A-G. Characterization of Fluorescence Activated Cell
Sorted and Manually Derived IPSC Lines by Sendai virus.
Immunofluroescence microscopy of the 1001.131.01 line demonstrating
expression of common markers of pluripotency by FACS or Manually
Derived IPSC lines. Nuclear Transcription Factors shown in Green,
Surface Markers shown in Red, Nucleus stained with DAPI in Blue (A)
Nanog/Tra-1-60 (B) Oct4/Tra-1-81 (C) Sox2/SSEA4 (D) Oct4/Alkaline
Phosphatase. 10.times. Magnification (E) Expression of endogenous
pluripotent transcription factors (F) Silencing of viral
transcription factors occur by passage 5. (G) Expression levels of
transcription factors common to the indicated germ layers from EB
generated by the indicated IPSC lines.
[0044] FIG. 17. Time Course analysis of retroviral reprogrammed
fibroblasts. The 0825 foreskin fibroblast line was analyzed for
changes in pluripotent surface marker expression by flow cytometry
at .about.7 dpi intervals following retroviral reprogramming to
determine earliest time point at which the
CD13.sup.NEGSSEA4.sup.POSTra-1-60.sup.POS population appears.
Values indicate percent of total cells in the culture expressing
the indicated markers.
[0045] FIGS. 18A-B. Karyotype of FACS and Manually Derived
retroviral iPS lines possess a normal karyotype and match the
parent fibroblast. Karyotype was assessed using 20 G-banded
metaphase cells from each fibroblast and reprogrammed lines at
passages indicated. All lines possess a normal karyotype and match
the parent fibroblast. Karyotype was assessed using 20 G-banded
metaphase cells from each fibroblast and reprogrammed lines at
passages indicated. Fibroblasts and FACS derived lines possess a
normal karyotype and match the parent fibroblast. Three out of 20
cells from the manually derived line displayed an unbalanced
translocation between the short arm of chromosomes 11 and 22
resulting in trisomy of the short arm of chromosome 11.
[0046] FIGS. 19A-D. FACS and Manually Derived Sendai iPS lines
express pluripotency markers. FACS (A) or Manually (B) derived
clones were expanded on MEF feeder layers and stained for two
common markers of pluripotency: Tra-1-60 and Nanog. 10.times.
Magnification. All lines show consistent expression of pluripotency
markers. (C) qRTPCR showing expression of endogenous gene
expression and silencing (D) of retroviral genes.
[0047] FIGS. 20A-G. Automated fibroblast and iPSC production. (A)
Schematic of workflow through automation system from donor biopsy
collection through to iPS expansion and freezing. (B) Image of
system for automated fibroblast production consisting of a liquid
handling device, imager, centrifuge and capper/decaper contained in
a biosafety cabinet, connected to an automated incubator and
managed by system control software. (C) Phase contrast image of
representative fibroblast outgrowth from a biopsy. (10.times.) (D)
Fibroblast biopsy outgrowth (i) as visualized following automated
imaging. Confluence measurements (ii) and Hoechst stained nuclei
(iii) are compared against each other to generate a regression
model (iv) for calculating count values from unstained samples with
confluence measurements. (E) Histogram of fibroblast doubling times
calculated from confluence scans of fibroblasts during expansion.
(F) Scatterplot of doubling time vs. age of donor. (G) Fibroblast
doubling times from fibroblasts thawed and recovered for
reprogramming.
[0048] FIGS. 21A-I. Automated reprogramming. (A) Experimental
scheme for automated fibroblast thawing and reprogramming. (B)
Image of robotic system for automated fibroblast thawing and mRNA
transfections. (C) Timecourse of mRNA transfection showing
development of colonies over 22 days. (D) Image-based
identification and counting of TRA-1-60 positive colonies to
determine reprogramming efficiency. (E) FACS analysis of
reprogrammed cultures from automated mRNA transfection
demonstrating that higher proportion of cells after reprogramming
by mRNA stain double positive for the pluripotency markers
TRA-1-60/SSEA4 and lack of the fibroblast surface marker CD13.
(F-I) Effect plots of poisson regression analysis of factors that
contribute to reprogramming success. Gray area and bars indicate
confidence intervals.
[0049] FIGS. 22A-G. Automated iPSC purification and arraying. (A)
Schematic illustration of bulk method of unreprogrammed fibroblast
cell depletion from reprogramming 24 well plates, consolidation and
freezing. (B) Image of integrated magnetic bead selection robot.
(C) Representative images of 96-well for bulk sorted cells from
first day post sorting (1 dps) to 9 days post sorting (9 dps), and
TRA-1-60 expression pattern captured by automated imaging. (D)
Example of a 96-well plate of sorted iPSCs derived from mRNA
mediated reprogramming. Three samples are represented on the plate
in three-point two fold serial dilution. (E) Representative images
for retrospective identification of clonal lines derived from
sorted cells from a single cell identified on the second day post
sorting (2 dps) to its colony at 10 days post sorting (10 dps), and
TRA-1-60 expression pattern captured by Celigo Tumorsphere
application. (F) FACS analysis for TRA-1-60/SSEA4/CD13 on sorted
cells after consolidation and prior to freezing. (G) Histogram of
doubling time for iPSCs during growth after sorting before
freezing. Frequency bins are 6 hrs. Median doubling time was 42 hr,
n=826 samples.
[0050] FIGS. 23A-B. Gene expression analysis of sorted cells. (A)
Boxplot of the pluripotency scores for reference hESC lines, iPSC
lines, and fibroblast lines. (B) Boxplot of differentiation scores
for the three categories of cell lines.
[0051] FIGS. 24A-F. Automated parallel iPSC culture. (A) Image of
96-well freezing and passaging robot. (B) Bright field images of
iPS cells in the same well in a 96W plate recovering after
automated thawing method. Confluence was monitored over 5 days. (C)
Correlation of confluence data from the Celigo prior to cryotube
freeze and post-thaw. Both the freezing and thawing of cryotubes
were performed on the integrated automated system. (D) FACS
analysis of TRA-1-60/SSEA4 double positive population before and
after automated passaging for control hESCs and iPSCs derived on
the system. (E) FACS analysis of iPSCs before freezing and
recovered from thawing using automated methods. (F) Example growth
rates of a robotically passaged iPSC plate over 3 days culture.
[0052] FIGS. 25A-F. Automated Embryoid body assay. (A) Boxplot of
the differentiation propensities (EC=ectoderm, ME=mesoderm,
EN=endoderm) for the 10 hESC reference lines with segments showing
the average differentiation propensities observed for iPSC lines
derived using three different methods. (B) Representative image of
the Greiner 96 well v-bottom plate with EBs is shown after passage
to form EBs by automation. The EBs were generated from iPSC lines
ubiquotously expressing GFP. (C) Image of EBs by stereomicroscopy.
(D-F) Correlation of differentiation propensity for all samples
generated using the reference lines used in this study with
previously published scorecard reference data (Bock et al.,
2011).
[0053] FIG. 26. Reduced variation in robotically derived iPSCs.
Variance analysis of scorecard gene expression in EBs showing
comparisons of standard deviation of gene expression values among
samples derived on and off the automated system. Lines produced by
the automated process showed significantly less variation in EB
gene expression compared to lines produced by manual methods and
later introduced onto the system (p value=7.08E-12, Wilcoxen signed
rank test). The comparison between manually derived lines and lines
reprogrammed on the automation but with manual colony picking was
marginally significantly different (p value=0.023)*=p<0.05,
***=p<0.001).
[0054] FIGS. 27A-B. (A) Mycoplasma detection of samples from
in-house automated luminescence assay. Marginal values were
confirmed negative with PCR validation. No mycoplasma positive
samples have been generated in house during biopsy collection and
outgrowth expansion on the automated systems. (B) Representative
traces of fibroblasts karyotyped using the Nanostring Karyotype
assay with representative traces of normal diploid fibroblasts (a)
46, XX, (b) 46, XY and an aneuploid fibroblast showing a loss of
one X chromosome (c) 45, X.
[0055] FIGS. 28A-E. Comparisons of automated reprogramming by mRNA
and Sendai. (A) Pluripotency staining of mRNA derived lines and
example of a phase contrast image of iPSC produced by mRNA
transfection. Scale bars are 50 .mu.m. (B) Well image of Sendai
reprogramming after 20 days showing colonies and TRA-1-60 live
stain of the same well in the bottom panel. Only a subset of
colonies stain positive for the pluripotency marker. (C)
Pluripotency marker staining of established cell lines from
automated reprogramming by Sendai virus. Scale bars are 50 .mu.m.
(D) FACS analysis of reprogrammed cultures from automated mRNA
transfection demonstrating that higher proportion of cells after
reprogramming by mRNA stain double positive for the pluripotency
markers TRA-1-60/SSEA4 and lack of the fibroblast surface marker
CD13. (E) Variation of gene expression of the germ layer and
pluripotency markers shown in (D) for BJ fibroblasts reprogrammed
on the automated system by mRNA transfection or Sendai infection
and isolated by manual colony picking Means are not significantly
different. N=33.
[0056] FIGS. 29A-C. (A) iPSC:fibroblast (1:20 to 1:100) were mixed,
5% of total cells before and after magnetic bead negative selection
using anti-fibroblast microbeads were analyzed using FACS.
Representative data is shown pre and post-sort of a mixture of
iPSCs and adult human fibroblasts at a 1:50 ratio. (B)
Representative FACS result for 5% of total cells before and after
magnetic bead negative selection using anti-fibroblast microbeads.
(C) Examples of clonal lines derived by automated sorting
method.
[0057] FIGS. 30A-C. (A) Pluri25 scorecard assay values for T scores
and gene expression means. (B) Immunofluoresence result for Nanog
expression in consolidated cells in 96 well format. (C) Example of
overgrown well demonstrating spontaneous differentiation detectible
by the Pluri25 scorecard assays.
[0058] FIGS. 31A-H. (A) Schematic of thawing and passaging and
plate replication in 96 well format. (B) Percent coefficient of
variation was calculated for 3 plates from the replication passages
of a representative cell line using data from confluence scans from
3 different time points. (C) Immunostaining of iPS lines derived on
the robotic platform as well as control hES cell lines showing the
presence of POU5FI and TRA.sub.--1-81; SSEA4 and NANOG, and SOX2
and TRA-1-81. (D) FACS analysis of TRA-1-60/SSEA4 double positive
population before and after automated passage 1:3 for control hESC
lines and iPSC lines derived on the system. (E) Detection of an
aneuploid line in 4 of 38 independent iPSC lines tested using the
Nanostring karyotyping assay. (F-H) Nanostring identity test data
comparing Fibroblast lines to iPSCs derived by the automated
process.
[0059] FIGS. 32A-B. (A) Pluripotency marker analysis of reference
lines used for lineage scorecard analysis after adaptation to
serum-free media used to grow iPSCs on the system. EBs were
generated from these lines by the automated system under identical
conditions to those used to generate EBs from iPSCs generated on
the system. (B) Scorecard analysis of EBs generated from reference
HUES lines under automated conditions.
[0060] FIGS. 33A-B. (A) Comparisons of standard deviation of gene
expression values for different types of cell lines considering
only a single replicate per sample. (B) Significance test: -log
10(p-value) using the Wilcoxen signed rank test that tests the null
hypothesis that the median of these paired distributions is the
same (non-parametric test).
DETAILED DESCRIPTION
[0061] The present invention provides various improved systems and
methods for obtaining, generating, culturing, and handling cells,
such as stem cells (including induced pluripotent stem cells or
iPSCs) and differentiated cells, as well as cells and cell panels
produced using such systems and methods, and uses of such cells and
cell panels. The present invention builds upon, and provides
certain improvements over, the systems and methods described
previously in international patent application PCT/US2012/067417
(published on Jun. 6, 2013 with publication number WO/2013/082509)
and U.S. patent application Ser. No. 13/691,258 (published on Dec.
26, 2013 with publication number 2013-0345094), the contents of
each of which are hereby incorporated by reference in their
entireties for those jurisdictions that permit incorporation by
reference. Building on the work described in these prior patent
applications, the Applicants have now developed certain improved
methods and systems that can significantly reduce variability in
obtaining, generating, culturing, and handling a variety of cell
types, including differentiated cells and stem cells. Such improved
systems and methods are particularly advantageous for automated
and/or high-throughput applications--greatly facilitating the
ability to work with large numbers of cells in a parallel
manner.
[0062] Several of the major embodiments of the present invention
are described in the above "Summary of the Invention" section of
this application, as well as in the Examples, Figures, and Claims
sections of this patent application. In order to avoid unnecessary
duplication, such embodiments may not be described in full in this
Detailed Description section. Rather this Detailed Description
provides certain additional information regarding the invention,
which is intended to be read together and in conjunction with the
Summary of the Invention section of the application and all other
sections of this patent application. Furthermore, the various
embodiments described in each section of this patent application
are intended to be combined in various ways, as will be apparent to
those of skill in the art.
[0063] As used herein "adult" means post-fetal, i.e., an organism
from the neonate stage through the end of life, and includes, for
example, cells obtained from delivered placenta tissue, amniotic
fluid and/or cord blood.
[0064] As used herein, the term "adult differentiated cell"
encompasses a wide range of differentiated cell types obtained from
an adult organism, that are amenable to producing iPSCs using the
instantly described automation system. Preferably, the adult
differentiated cell is a "fibroblast." Fibroblasts, also referred
to as "fibrocytes" in their less active form, are derived from
mesenchyme. Their function includes secreting the precursors of
extracellular matrix components including, e.g., collagen.
Histologically, fibroblasts are highly branched cells, but
fibrocytes are generally smaller and are often described as
spindle-shaped. Fibroblasts and fibrocytes derived from any tissue
may be employed as a starting material for the automated workflow
system on the invention.
[0065] As used herein, the term, "induced pluripotent stem cells"
or, iPSCs, means that the stem cells are produced from
differentiated adult cells that have been induced or changed, i.e.,
reprogrammed into cells capable of differentiating into tissues of
all three germ or dermal layers: mesoderm, endoderm, and ectoderm.
The iPSCs produced do not refer to cells as they are found in
nature.
[0066] Mammalian "somatic cells" useful in the present invention
include, by way of example, adult stem cells, sertoli cells,
endothelial cells, granulosa epithelial cells, neurons, pancreatic
islet cells, epidermal cells, epithelial cells, hepatocytes, hair
follicle cells, keratinocytes, hematopoietic cells, melanocytes,
chondrocytes, lymphocytes (B and T lymphocytes), erythrocytes,
macrophages, monocytes, mononuclear cells, fibroblasts, cardiac
muscle cells, other known muscle cells, and generally any live
somatic cells. In particular embodiments, fibroblasts are used. The
term somatic cell, as used herein, is also intended to include
adult stem cells. An adult stem cell is a cell that is capable of
giving rise to all cell types of a particular tissue. Exemplary
adult stem cells include hematopoietic stem cells, neural stem
cells, and mesenchymal stem cells.
[0067] The term "totipotency" refers to a cell with a developmental
potential to make all of the cells in the adult body as well as the
extra-embryonic tissues, including the placenta. The fertilized egg
(zygote) is totipotent, as are the cells (blastomeres) of the
morula (up to the 16-cell stage following fertilization).
[0068] The term "pluripotent" as used herein refers to a cell with
the developmental potential, under different conditions, to
differentiate to cell types characteristic of all three germ cell
layers, i.e., endoderm (e.g., gut tissue), mesoderm (including
blood, muscle, and vessels), and ectoderm (such as skin and nerve).
A pluripotent cell has a lower developmental potential than a
totipotent cell. The ability of a cell to differentiate to all
three germ layers can be determined using, for example, a nude
mouse teratoma formation assay. In some embodiments, pluripotency
can also evidenced by the expression of embryonic stem (ES) cell
markers, although the preferred test for pluripotency of a cell or
population of cells generated using the compositions and methods
described herein is the demonstration that a cell has the
developmental potential to differentiate into cells of each of the
three germ layers. In some embodiments, a pluripotent cell is
termed an "undifferentiated cell." Accordingly, the terms
"pluripotency" or a "pluripotent state" as used herein refer to the
developmental potential of a cell that provides the ability for the
cell to differentiate into all three embryonic germ layers
(endoderm, mesoderm and ectoderm). Those of skill in the art are
aware of the embryonic germ layer or lineage that gives rise to a
given cell type. A cell in a pluripotent state typically has the
potential to divide in vitro for a long period of time, e.g.,
greater than one year or more than 30 passages.
[0069] The term "multipotent" when used in reference to a
"multipotent cell" refers to a cell that has the developmental
potential to differentiate into cells of one or more germ layers,
but not all three. Thus, a multipotent cell can also be termed a
"partially differentiated cell." Multipotent cells are well known
in the art, and examples of multipotent cells include adult stem
cells, such as for example, hematopoietic stem cells and neural
stem cells. "Multipotent" indicates that a cell may form many types
of cells in a given lineage, but not cells of other lineages. For
example, a multipotent hematopoietic cell can form the many
different types of blood cells (red, white, platelets, etc.), but
it cannot form neurons. Accordingly, the term "multipotency" refers
to a state of a cell with a degree of developmental potential that
is less than totipotent and pluripotent.
[0070] The terms "stem cell" or "undifferentiated cell" as used
herein, refer to a cell in an undifferentiated or partially
differentiated state that has the property of self-renewal and has
the developmental potential to differentiate into multiple cell
types, without a specific implied meaning regarding developmental
potential (i.e., totipotent, pluripotent, multipotent, etc.). A
stem cell is capable of proliferation and giving rise to more such
stem cells while maintaining its developmental potential. In
theory, self-renewal can occur by either of two major mechanisms.
Stem cells can divide asymmetrically, which is known as obligatory
asymmetrical differentiation, with one daughter cell retaining the
developmental potential of the parent stem cell and the other
daughter cell expressing some distinct other specific function,
phenotype and/or developmental potential from the parent cell. The
daughter cells themselves can be induced to proliferate and produce
progeny that subsequently differentiate into one or more mature
cell types, while also retaining one or more cells with parental
developmental potential. A differentiated cell may derive from a
multipotent cell, which itself is derived from a multipotent cell,
and so on. While each of these multipotent cells may be considered
stem cells, the range of cell types each such stem cell can give
rise to, i.e., their developmental potential, can vary
considerably. Alternatively, some of the stem cells in a population
can divide symmetrically into two stem cells, known as stochastic
differentiation, thus maintaining some stem cells in the population
as a whole, while other cells in the population give rise to
differentiated progeny only. Accordingly, the term "stem cell"
refers to any subset of cells that have the developmental
potential, under particular circumstances, to differentiate to a
more specialized or differentiated phenotype, and which retain the
capacity, under certain circumstances, to proliferate without
substantially differentiating. In some embodiments, the term stem
cell refers generally to a naturally occurring parent cell whose
descendants (progeny cells) specialize, often in different
directions, by differentiation, e.g., by acquiring completely
individual characters, as occurs in progressive diversification of
embryonic cells and tissues. Some differentiated cells also have
the capacity to give rise to cells of greater developmental
potential. Such capacity may be natural or may be induced
artificially upon treatment with various factors. Cells that begin
as stem cells might proceed toward a differentiated phenotype, but
then can be induced to "reverse" and re-express the stem cell
phenotype, a term often referred to as "dedifferentiation" or
"reprogramming" or "retrodifferentiation" by persons of ordinary
skill in the art.
[0071] The term "embryonic stem cell" as used herein refers to
naturally occurring pluripotent stem cells of the inner cell mass
of the embryonic blastocyst (see, for e.g., U.S. Pat. Nos.
5,843,780; 6,200,806; 7,029,913; 7,584,479, which are incorporated
herein by reference). Such cells can similarly be obtained from the
inner cell mass of blastocysts derived from somatic cell nuclear
transfer (see, for example, U.S. Pat. Nos. 5,945,577, 5,994,619,
6,235,970, which are incorporated herein by reference). Embryonic
stem cells are pluripotent and give rise during development to all
derivatives of the three primary germ layers: ectoderm, endoderm
and mesoderm. In other words, they can develop into each of the
more than 200 cell types of the adult body when given sufficient
and necessary stimulation for a specific cell type. They do not
contribute to the extra-embryonic membranes or the placenta, i.e.,
are not totipotent.
[0072] As used herein, the distinguishing characteristics of an
embryonic stem cell define an "embryonic stem cell phenotype."
Accordingly, a cell has the phenotype of an embryonic stem cell if
it possesses one or more of the unique characteristics of an
embryonic stem cell, such that that cell can be distinguished from
other cells not having the embryonic stem cell phenotype. Exemplary
distinguishing embryonic stem cell phenotype characteristics
include, without limitation, expression of specific cell-surface or
intracellular markers, including protein and microRNAs, gene
expression profiles, methylation profiles, deacetylation profiles,
proliferative capacity, differentiation capacity, karyotype,
responsiveness to particular culture conditions, and the like. In
some embodiments, the determination of whether a cell has an
"embryonic stem cell phenotype" is made by comparing one or more
characteristics of the cell to one or more characteristics of an
embryonic stem cell line cultured within the same laboratory.
[0073] The term "somatic stem cell" is used herein to refer to any
pluripotent or multipotent stem cell derived from non-embryonic
tissue, including fetal, juvenile, and adult tissue. Natural
somatic stem cells have been isolated from a wide variety of adult
tissues including blood, bone marrow, brain, olfactory epithelium,
skin, pancreas, skeletal muscle, and cardiac muscle. Each of these
somatic stem cells can be characterized based on gene expression,
factor responsiveness, and morphology in culture. Exemplary
naturally occurring somatic stem cells include, but are not limited
to, neural stem cells, neural crest stem cells, mesenchymal stem
cells, hematopoietic stem cells, and pancreatic stem cells. In some
aspects described herein, a "somatic pluripotent cell" refers to a
somatic cell, or a progeny cell of the somatic cell, that has had
its developmental potential altered, i.e., increased, to that of a
pluripotent state by contacting with, or the introduction of, one
or more reprogramming factors using the compositions and methods
described herein.
[0074] The term "progenitor cell" is used herein to refer to cells
that have greater developmental potential, i.e., a cellular
phenotype that is more primitive (e.g., is at an earlier step along
a developmental pathway or progression) relative to a cell which it
can give rise to by differentiation. Often, progenitor cells have
significant or very high proliferative potential. Progenitor cells
can give rise to multiple distinct cells having lower developmental
potential, i.e., differentiated cell types, or to a single
differentiated cell type, depending on the developmental pathway
and on the environment in which the cells develop and
differentiate.
[0075] As used herein, the term "somatic cell" refers to any cell
other than a germ cell, a cell present in or obtained from a
pre-implantation embryo, or a cell resulting from proliferation of
such a cell in vitro. Stated another way, a somatic cell refers to
any cell forming the body of an organism, as opposed to a germline
cell. In mammals, germline cells (also known as "gametes") are the
spermatozoa and ova which fuse during fertilization to produce a
cell called a zygote, from which the entire mammalian embryo
develops. Every other cell type in the mammalian body--apart from
the sperm and ova, the cells from which they are made (gametocytes)
and undifferentiated, pluripotent, embryonic stem cells--is a
somatic cell: internal organs, skin, bones, blood, and connective
tissue are all made up of somatic cells. In some embodiments the
somatic cell is a "non-embryonic somatic cell," by which is meant a
somatic cell that is not present in or obtained from an embryo and
does not result from proliferation of such a cell in vitro. In some
embodiments the somatic cell is an "adult somatic cell," by which
is meant a cell that is present in or obtained from an organism
other than an embryo or a fetus or results from proliferation of
such a cell in vitro. Unless otherwise indicated, the compositions
and methods for reprogramming a somatic cell described herein can
be performed both in vivo and in vitro (where in vivo is practiced
when a somatic cell is present within a subject, and where in vitro
is practiced using an isolated somatic cell maintained in
culture).
[0076] The term "differentiated cell" encompasses any somatic cell
that is not, in its native form, pluripotent, as that term is
defined herein. Thus, the term a "differentiated cell" also
encompasses cells that are partially differentiated, such as
multipotent cells, or cells that are stable, non-pluripotent
partially reprogrammed, or partially differentiated cells,
generated using any of the compositions and methods described
herein. In some embodiments, a differentiated cell is a cell that
is a stable intermediate cell, such as a non-pluripotent, partially
reprogrammed cell. It should be noted that placing many primary
cells in culture can lead to some loss of fully differentiated
characteristics. Thus, simply culturing such differentiated or
somatic cells does not render these cells non-differentiated cells
(e.g. undifferentiated cells) or pluripotent cells. The transition
of a differentiated cell (including stable, non-pluripotent
partially reprogrammed cell intermediates) to pluripotency requires
a reprogramming stimulus beyond the stimuli that lead to partial
loss of differentiated character upon placement in culture.
Reprogrammed and, in some embodiments, partially reprogrammed
cells, also have the characteristic of having the capacity to
undergo extended passaging without loss of growth potential,
relative to parental cells having lower developmental potential,
which generally have capacity for only a limited number of
divisions in culture. In some embodiments, the term "differentiated
cell" also refers to a cell of a more specialized cell type (i.e.,
decreased developmental potential) derived from a cell of a less
specialized cell type (i.e., increased developmental potential)
(e.g., from an undifferentiated cell or a reprogrammed cell) where
the cell has undergone a cellular differentiation process.
[0077] The term "reprogramming" as used herein refers to a process
that reverses the developmental potential of a cell or population
of cells (e.g., a somatic cell). Stated another way, reprogramming
refers to a process of driving a cell to a state with higher
developmental potential, i.e., backwards to a less differentiated
state. The cell to be reprogrammed can be either partially or
terminally differentiated prior to reprogramming. In some
embodiments of the aspects described herein, reprogramming
encompasses a complete or partial reversion of the differentiation
state, i.e., an increase in the developmental potential of a cell,
to that of a cell having a pluripotent state. In some embodiments,
reprogramming encompasses driving a somatic cell to a pluripotent
state, such that the cell has the developmental potential of an
embryonic stem cell, i.e., an embryonic stem cell phenotype. In
some embodiments, reprogramming also encompasses a partial
reversion of the differentiation state or a partial increase of the
developmental potential of a cell, such as a somatic cell or a
unipotent cell, to a multipotent state. Reprogramming also
encompasses partial reversion of the differentiation state of a
cell to a state that renders the cell more susceptible to complete
reprogramming to a pluripotent state when subjected to additional
manipulations, such as those described herein. Such manipulations
can result in endogenous expression of particular genes by the
cells, or by the progeny of the cells, the expression of which
contributes to or maintains the reprogramming. In certain
embodiments, reprogramming of a cell using the synthetic, modified
RNAs and methods thereof described herein causes the cell to assume
a multipotent state (e.g., is a multipotent cell). In some
embodiments, reprogramming of a cell (e.g. a somatic cell) using
the synthetic, modified RNAs and methods thereof described herein
causes the cell to assume a pluripotent-like state or an embryonic
stem cell phenotype. The resulting cells are referred to herein as
"reprogrammed cells," "somatic pluripotent cells," and "RNA-induced
somatic pluripotent cells." The term "partially reprogrammed
somatic cell" as referred to herein refers to a cell which has been
reprogrammed from a cell with lower developmental potential by the
methods as disclosed herein, such that the partially reprogrammed
cell has not been completely reprogrammed to a pluripotent state
but rather to a non-pluripotent, stable intermediate state. Such a
partially reprogrammed cell can have a developmental potential
lower that a pluripotent cell, but higher than a multipotent cell,
as those terms are defined herein. A partially reprogrammed cell
can, for example, differentiate into one or two of the three germ
layers, but cannot differentiate into all three of the germ
layers.
[0078] The term a "reprogramming factor," as used herein, refers to
a developmental potential altering factor, as that term is defined
herein, such as a gene, protein, RNA, DNA, or small molecule, the
expression of which contributes to the reprogramming of a cell,
e.g. a somatic cell, to a less differentiated or undifferentiated
state, e.g. to a cell of a pluripotent state or partially
pluripotent state. A reprogramming factor can be, for example,
transcription factors that can reprogram cells to a pluripotent
state, such as SOX2, OCT3/4, KLF4, NANOG, LIN-28, c-MYC, and the
like, including as any gene, protein, RNA or small molecule, that
can substitute for one or more of these in a method of
reprogramming cells in vitro. In some embodiments, exogenous
expression of a reprogramming factor, using the synthetic modified
RNAs and methods thereof described herein, induces endogenous
expression of one or more reprogramming factors, such that
exogenous expression of one or more reprogramming factors is no
longer required for stable maintenance of the cell in the
reprogrammed or partially reprogrammed state. "Reprogramming to a
pluripotent state in vitro" is used herein to refer to in vitro
reprogramming methods that do not require and/or do not include
nuclear or cytoplasmic transfer or cell fusion, e.g., with oocytes,
embryos, germ cells, or pluripotent cells. A reprogramming factor
can also be termed a "de-differentiation factor," which refers to a
developmental potential altering factor, as that term is defined
herein, such as a protein or RNA, that induces a cell to
de-differentiate to a less differentiated phenotype, that is a
de-differentiation factor increases the developmental potential of
a cell.
[0079] As used herein, the term "differentiation factor" refers to
a developmental potential altering factor, as that term is defined
herein, such as a protein, RNA, or small molecule, that induces a
cell to differentiate to a desired cell-type, i.e., a
differentiation factor reduces the developmental potential of a
cell. In some embodiments, a differentiation factor can be a
cell-type specific polypeptide, however this is not required.
Differentiation to a specific cell type can require simultaneous
and/or successive expression of more than one differentiation
factor. In some aspects described herein, the developmental
potential of a cell or population of cells is first increased via
reprogramming or partial reprogramming using synthetic, modified
RNAs, as described herein, and then the cell or progeny cells
thereof produced by such reprogramming are induced to undergo
differentiation by contacting with, or introducing, one or more
synthetic, modified RNAs encoding differentiation factors, such
that the cell or progeny cells thereof have decreased developmental
potential.
[0080] In the context of cell ontogeny, the term "differentiate",
or "differentiating" is a relative term that refers to a
developmental process by which a cell has progressed further down a
developmental pathway than its immediate precursor cell. Thus in
some embodiments, a reprogrammed cell as the term is defined
herein, can differentiate to a lineage-restricted precursor cell
(such as a mesodermal stem cell), which in turn can differentiate
into other types of precursor cells further down the pathway (such
as a tissue specific precursor, for example, a cardiomyocyte
precursor), and then to an end-stage differentiated cell, which
plays a characteristic role in a certain tissue type, and may or
may not retain the capacity to proliferate further.
[0081] As used herein, the term "without the formation of a
pluripotent intermediate cell" refers to the transdifferentiation
of one cell type to another cell type, preferably, in one step;
thus a method that modifies the differentiated phenotype or
developmental potential of a cell without the formation of a
pluripotent intermediate cell does not require that the cell be
first dedifferentiated (or reprogrammed) and then differentiated to
another cell type. Instead, the cell type is merely "switched" from
one cell type to another without going through a less
differentiated phenotype. Accordingly, transdifferentiation refers
to a change in the developmental potential of a cell whereby the
cell is induced to become a different cell having a similar
developmental potential, e.g., a liver cell to a pancreatic cell, a
pancreatic alpha cell into a pancreatic beta cell, etc. The system
and methods of the invention are well suited for
transdifferentiation of cells.
[0082] The term "expression" refers to the cellular processes
involved in producing RNA and proteins and as appropriate,
secreting proteins, including where applicable, but not limited to,
for example, transcription, translation, folding, modification and
processing. "Expression products" include RNA transcribed from a
gene, and polypeptides obtained by translation of mRNA transcribed
from a gene. In some embodiments, an expression product is
transcribed from a sequence that does not encode a polypeptide,
such as a microRNA.
[0083] As used herein, the term "transcription factor" refers to a
protein that binds to specific parts of DNA using DNA binding
domains and is part of the system that controls the transcription
of genetic information from DNA to RNA.
[0084] As used herein, the term "small molecule" refers to a
chemical agent which can include, but is not limited to, a peptide,
a peptidomimetic, an amino acid, an amino acid analog, a
polynucleotide, a polynucleotide analog, an aptamer, a nucleotide,
a nucleotide analog, an organic or inorganic compound (e.g.,
including heterorganic and organometallic compounds) having a
molecular weight less than about 10,000 grams per mole, organic or
inorganic compounds having a molecular weight less than about 5,000
grams per mole, organic or inorganic compounds having a molecular
weight less than about 1,000 grams per mole, organic or inorganic
compounds having a molecular weight less than about 500 grams per
mole, and salts, esters, and other pharmaceutically acceptable
forms of such compounds.
[0085] The term "exogenous" as used herein refers to a nucleic acid
(e.g., a synthetic, modified RNA encoding a transcription factor),
or a protein (e.g., a transcription factor) that has been
introduced by a process involving the hand of man into a biological
system such as a cell or organism in which it is not normally
found, or in which it is found in lower amounts. A factor (e.g. a
synthetic, modified RNA encoding a transcription factor, or a
protein, e.g., a polypeptide) is considered exogenous if it is
introduced into an immediate precursor cell or a progeny cell that
inherits the substance. In contrast, the term "endogenous" refers
to a factor or expression product that is native to the biological
system or cell (e.g., endogenous expression of a gene, such as,
e.g., SOX2 refers to production of a SOX2 polypeptide by the
endogenous gene in a cell). In some embodiments, the introduction
of one or more exogenous factors to a cell, e.g., a developmental
potential altering factor, using the compositions and methods
comprising synthetic, modified RNAs described herein, induces
endogenous expression in the cell or progeny cell(s) thereof of a
factor or gene product necessary for maintenance of the cell or
progeny cell(s) thereof in a new developmental potential.
[0086] The term "isolated cell" as used herein refers to a cell
that has been removed from an organism in which it was originally
found, or a descendant of such a cell. Optionally the cell has been
cultured in vitro, e.g., in the presence of other cells.
Optionally, the cell is later introduced into a second organism or
re-introduced into the organism from which it (or the cell or
population of cells from which it descended) was isolated.
[0087] The term "isolated population" with respect to an isolated
population of cells as used herein refers to a population of cells
that has been removed and separated from a mixed or heterogeneous
population of cells. In some embodiments, an isolated population is
a "substantially pure" population of cells as compared to the
heterogeneous population from which the cells were isolated or
enriched. In some embodiments, the isolated population is an
isolated population of pluripotent cells which comprise a
substantially pure population of pluripotent cells as compared to a
heterogeneous population of somatic cells from which the
pluripotent cells were derived.
[0088] As used herein, the terms "synthetic, modified RNA" or
"modified RNA" refer to an RNA molecule produced in vitro, which
comprise at least one modified nucleoside as that term is defined
herein below. Methods of the invention do not require modified RNA.
The synthetic, modified RNA composition does not encompass mRNAs
that are isolated from natural sources such as cells, tissue,
organs etc., having those modifications, but rather only synthetic,
modified RNAs that are synthesized using in vitro techniques. The
term "composition," as applied to the terms "synthetic, modified
RNA" or "modified RNA," encompasses a plurality of different
synthetic, modified RNA molecules (e.g., at least 2, at least 3, at
least 4, at least 5, at least 6, at least 7, at least 8, at least
9, at least 10, at least 11, at least 12, at least 13, at least 14,
at least 15, at least 16, at least 17, at least 18, at least 19, at
least 20, at least 25, at least 30, at least 40, at least 50, at
least 75, at least 90, at least 100 synthetic, modified RNA
molecules or more). In some embodiments, a synthetic, modified RNA
composition can further comprise other agents (e.g., an inhibitor
of interferon expression or activity, a transfection reagent,
etc.). Such a plurality can include synthetic, modified RNA of
different sequences (e.g., coding for different polypeptides),
synthetic, modified RNAs of the same sequence with differing
modifications, or any combination thereof.
[0089] As used herein, the term "polypeptide" refers to a polymer
of amino acids comprising at least 2 amino acids (e.g., at least 5,
at least 10, at least 20, at least 30, at least 40, at least 50, at
least 60, at least 70, at least 80, at least 90, at least 100, at
least 125, at least 150, at least 175, at least 200, at least 225,
at least 250, at least 275, at least 300, at least 350, at least
400, at least 450, at least 500, at least 600, at least 700, at
least 800, at least 900, at least 1000, at least 2000, at least
3000, at least 4000, at least 5000, at least 6000, at least 7000,
at least 8000, at least 9000, at least 10,000 amino acids or more).
The terms "protein" and "polypeptide" are used interchangeably
herein. As used herein, the term "peptide" refers to a relatively
short polypeptide, typically between about 2 and 60 amino acids in
length.
[0090] Microarrays and particularly "cell arrays" or "cell panels"
are currently needed for screening of large biomolecule libraries,
such as RNAs, DNAs, proteins and small molecules with respect to
their biological functions and for fundamental investigation of
cell and gene-functions. Many research facilities both in academia
and in industry need advanced high-density arrays to improve their
screening-efficiency, velocity and quality. Many screens will first
become possible or significantly more affordable with the
development of next generation microarrays and cell arrays/cell
panels, respectively. An invention array or cell panel should
typically fit onto a customary microtiter scaled plate to ensure
the usability of conventional microplate handling robots and
microscopes. In one embodiment cell arrays or cell panels can
comprise any collection of cell lines that need to be assayed as a
unit under identical conditions, for example where the only
variable is the genotype of the cell lines. An example could be a
collection of normal and disease specific iPSC lines, or their
differentiated derivatives, plated in microtiter plates in wells
adjacent to each other. The cell panels may comprise cells derived
from multiple individuals in any "population of interest" and can
be selected such that the cells (or individuals from whom the cells
are derived) are representative of the diversity of that population
of interest. The cells in the cell panels may be stem cells,
differentiated cells made from such stem cells, or differentiated
cells made by trans-differentiation from cells of another type
(e.g. by trans-differentiation). Such cell panels can be used, for
example, to probe the activity of a single factor (e.g. small
molecule) on multiple genotypes simultaneously to discover genotype
specific effects of that factor using the appropriate assays.
[0091] One advantage of the present invention is that it provides
methods and systems for generating an essentially limitless supply
of isogenic or synegenic human cells (such as iPSCs and
differentiated cells derived therefrom) that may be suitable for
transplantation, use in drug discovery assays, and/or for disease
modeling. Such cells (such as iPSCs) may be tailored specifically
to the patient, therefore, potentially obviating the significant
problem associated with current transplantation methods, such as,
rejection of the transplanted tissue, which may occur because of
host versus graft or graft versus host rejection. When utilized for
drug discovery the cells demonstrate each person's response to
chemicals when used in drug discovery or their individual
manifestation of diseases in disease models. Several kinds of iPSCs
or fully differentiated somatic cells prepared from iPSCs derived
from somatic cells derived from humans can be stored in an iPSC
bank as a library of cells, and one kind or more kinds of the iPSCs
in the library can be used for preparation of somatic cells,
tissues, or organs that are free of rejection by a patient to be
subjected to stem cell therapy.
[0092] In one embodiment the present invention provides methods of
making panels of cells or "cell panels" that are derived from
multiple individuals in a "population of interest" and that may, in
some embodiments, be representative of the diversity of that
population of interest. Such cell panels can be made, for example,
using the automated systems of the present invention or other
suitable systems known the art. The cells in the cell panels may be
somatic cells, stem cells, differentiated cells made from such stem
cells, or differentiated cells made by trans-differentiation from
cells of another type (e.g. by trans-differentiation). Such cell
panels can be made in multiple formats and can be frozen and stored
to form frozen banks of cell panels. Such cell panels may be useful
for a variety of different applications, including, but not limited
to, use in assays designed to screen for new drugs that might be
effective in a given population of interest, and/or to test the
efficacy, safety, and/or toxicity of drugs in a given population of
interest.
[0093] The cell panels of the present invention may include samples
obtained from, and/or be designed to be representative of, any
"population of interest" desired, including, but not limited to,
the world population, the population of a particular country, the
population of a particular continent, the population of a
particular geographic region (e.g. Northern Italian, Indian
sub-continent, etc.), the population of a particular racial or
ethnic group (e.g. Ashkenazi Jews, Maoris, etc.), a population of a
particular age, a population of a particular sex (male or female),
a population having a particular disease or disorder (e.g. a
specific cancer, metastatic cancer, Huntington disease, Parkinson's
disease, psoriasis, asthma, post-traumatic stress disorder,
traumatic brain injury, autism, or any other disease or disorder of
interest), a population having a particular mutation, a population
having a particular genotype, a population having a particular
phenotype, a population having a particular HLA type, a population
having a particular blood group, a population having a particular
drug response profile, and the like. In some embodiments the panels
of the present invention may be designed to be representative of
the population of interest (e.g. in terms or race, ethnicity, sex,
age, genotype, phenotype or any other desired characteristic), for
example based on population Census data. In some embodiments the
cell panels may comprise engineered lines, such as those created to
test for the effects of particular mutations.
[0094] For some applications it will be desirable to use "control"
panels of cells, or panels comprising "control" cells. Such
controls can be used for comparison to cells from the populations
of interest. For example, if a panel comprises cell samples having
a particular mutation (such as a mutation related to a particular
disease) it may desirable to have a control panel comprising
control cell samples, or to include control cell samples in the
panel. In some embodiments, such control cells samples may comprise
isogenic control cell samples, such as cell samples in which a
mutation has been corrected.
[0095] In some embodiments the present invention provides panels of
stem cells that are derived from multiple individuals in a
population of interest. In some embodiments the stem cells may
comprise induced pluripotent stem cells (iPSCs). Such panels can be
made, for example, by obtaining differentiated somatic cells from
an adult or child and using iPSC methods known in the art to
convert those cells to pluripotent stem cells, for example using
the automated systems of the invention. In some embodiments the
stem cells may comprise embryonic stem cell (ESCs), for example
ESCs derived from donated embryos (such as those created in an IVF
procedure) or ESCs made by a nuclear transfer technique.
[0096] In some embodiments the present invention provides panels of
differentiated cells that are derived from multiple individuals in
a population of interest. Types of differentiated cells that may be
provided using in the format of a panel according to the invention
include, but are not limited to: oligodendrocytes, beta cells,
cortical neurons, dopaminergic neurons, cardiomyocytes, and cells
of certain mesenchymal lineages (osteoblasts).
[0097] In some embodiments the cell panels of the present invention
are made in, and/or provided in, the form of tissue culture
vessels, such as tissue culture plates, bottles, or vials. In one
embodiment the cell panels of the present invention are made in,
and/or provided in, microtiter plates, such as those having 6, 24,
96, 384, 1536, 3456 or 9600 wells in one plate. In some
embodiments, each well in such a microtiter plate may comprise
cells derived from one individual (such as one human individual)
with every well containing cells from different individuals. For
example, 96 different individuals may be represented in one 96-well
plate, 384 different individuals may be represented in one 384-well
plate, and 1596 different individuals may be represented in one
1596-well plate within the population group of interest. In other
embodiments multiple wells within one plate may comprise cells from
the same individual.
[0098] In one embodiment the panels of the present invention are
made using an automation platform, such as that described herein or
in U.S. patent application Ser. No. 13/691,257, the contents of
which are hereby incorporated by reference. In other embodiments
these cell panels may be made manually or by any other suitable
means known in the art.
[0099] The cell panels of the present invention have a variety of
uses. In some embodiments the cell panels can be used for disease
modeling, drug screening, toxicology testing (e.g. for testing the
toxixicity of drugs on specific populations of interest), efficacy
studies (e.g. for testing efficacy of drugs on specific populations
of interest), studying basic biology, studying developmental
biology, for generating cell products (e.g. materials generated
using cells as "factories"), or identifying groups of individuals
similarly affected by drugs. As such, the cell panels can be used
in methods that resemble clinical trials but that are performed in
vitro, allowing drugs to be tested on cells from large cohorts of
different individuals. In this way it may be possible, for example,
to identify subgroups of individuals that respond in a particular
way to drugs before the drugs are used in clinical trials or are
approved and used in the population at large.
[0100] The cell panels of the present invention can be provided in
various forms. In one embodiment they can be provided as
growing/living cells, for example in the form of a microtiter
plate, or plates, of living cells. Such plates of living cells can
be passaged as needed to maintain, continue or expand the cell
panel(s). In some embodiments the plates of cells can be passaged
using an automated system such as that described herein. In some
embodiments the cell panels of the present invention are provided
as frozen cells, for example in one or more plates or vials. In
some embodiments the panels of the present invention may be frozen
and/or thawed using an automated system such as that described
herein.
[0101] In one aspect the present invention provides automated
systems suitable for generating, maintaining and handling a variety
types, such as iPSCs and differentiated cells produced therefrom.
The invention system greatly improves the efficiency and
reproducibility of making and handling standardized iPSC lines and
other cell lines. Typically, researchers generate iPSCs by hand,
which limits the cells utility due to researcher variability and an
inability to generate large numbers of cells. The invention system
circumvents these problems with a completely automated system from
receipt of the tissue or cell sample to banking of large stocks of
well-defined iPSC lines and/or differentiated cells produced
therefrom. The system allows for consistency in the generation of
large numbers of cells from many donors, which will facilitate the
use of iPSC technology to discover treatments and cures for many
diseases. Various embodiments and components of the automated
systems of the invention are described herein. In addition, each of
such embodiments can be modified by inclusion of a data-driven
batching system, or a component thereof, as described in other
sections of this patent application.
[0102] In one embodiment, the workflow system of the invention
includes an automated system for generating and isolating iPSCs,
comprising: a somatic cell, e.g., fibroblast, plating unit for
placing cells on a plate; and an induction unit for automated
reprogramming of cells by contacting the cells on the plating unit
with reprogramming factors to produce iPSCs. In some embodiments
the system further comprises a data-driven batching system, or a
component thereof. In a further embodiment, the invention system
includes a sorting unit for selectively sorting and isolating the
iPSCs produced by the induction unit by identifying iPSC specific
markers, including, e.g., surface markers or green fluorescent
proteins inserted by a transfection vector. Somatic cells can be
obtained from cell lines, biopsy or other tissue samples, including
blood, and the like.
[0103] In another embodiment, the invention provides an automated
system for generating and isolating differentiated adult cells from
stem cells, e.g., iPSCs, embryonic stem (ES) cells or mesenchymal
stem (MS) cells, comprising: a stem cell plating unit for placing
cells, e.g., iPSCs, ES or MS cells, on a plate; and an induction
unit for automated reprogramming of cells by contacting the cells
on the stem cell plating unit with reprogramming factors to produce
differentiated adult cells. In some embodiments the system further
comprises a data-driven batching system, or a component thereof. In
one embodiment, the system further includes a sorting unit for
selectively sorting and isolating the differentiated adult cells
produced by the induction unit by identifying markers specific to
the differentiated adult cells.
[0104] In yet another embodiment, the invention provides an
automated system for generating and isolating differentiated adult
cells from induced pluripotent stem cells (iPSCs), comprising: an
iPSC plating unit for placing iPSCs on a plate; and an induction
unit for automated reprogramming of iPSCs by contacting the iPSCs
on the iPSC plating unit with reprogramming factors to produce
differentiated adult cells. In some embodiments the system further
comprises a data-driven batching system, or a component thereof. In
one embodiment, the system further includes a sorting unit for
selectively sorting and isolating the differentiated adult cells
produced by the induction unit by identifying markers specific to
the differentiated adult cells.
[0105] The invention provides an automated workflow system for
producing iPSCs from differentiated adult cells. Broadly, the
inventive workflow system provides a new workflow system that
starts with adult differentiated cells (e.g., isolated or tissue
samples) and results in either iPSCs or adult cells derived from
pluripotent cells. In some embodiments the workflow system
comprises a data-driven batching system, or a component thereof. In
one embodiment, the adult differentiated cells are preferably
fibroblasts obtained, e.g., from skin biopsies. The adult
fibroblasts are converted into induced pluripotent stem cells
(iPSCs) by the inventive workflow that incorporates automation and
robotics. The inventive workflow system is capable of generating
thousands of iPSCs in parallel resulting in an accelerated
timeframe, in a period of months instead of the years, which would
have previously been required. The inventive workflow system can be
adapted to any cell isolation system for starting material and be
applied to direct or indirect reprogramming and
transdifferentiation, for example. The inventive workflow system
will allow production employing cellular arrays of cells from 6,
24, 96, 384, 1536 sized arrays, or greater (such as 3456 or 9600
sized arrays). The inventive workflow system is flexible and will
allow for multiple iterations and flexibility in cell type and
tissue. The description herein is shown with fibroblasts as an
illustrative somatic cell. As noted herein, other cell types are
used in the system. The example is not meant to be limited in this
way.
[0106] The Workflow System
[0107] The workflow system is broken down into four
independently-operated units: [0108] (1) Quarantine Somatic Cell
Isolation and Growth (System 1); [0109] (2) Quarantine Assay
(System 2); [0110] (3) Thawing, Infection and Identification
(Systems 3, 4, and 5); and [0111] (4) Maintenance, QC, Expansion,
and Freezing. (Systems 6, 7, and 8)
[0112] Additionally, an automated -80 storage and retrieval system
for storing fibroblasts and final clones in 1.4 mL Matrix screw cap
tubes, is part of the system. The systems, and the steps and
operations that each unit will perform, will be described
below.
[0113] System 1, Part A: Quarantine Somatic Cell Isolation and
Growth Workflow, Biopsy Processing Pre-Mycoplasma Test [0114] 1.
Technician will plate 40 biopsies per week in 6-well dishes; [0115]
2. 6-well plates will be maintained in quarantine incubator with
200-plate capacity; [0116] 3. Periodic confluency checks are
performed on an integrated Cyntellect Celigo Cytometer.
[0117] The system components that may be used to perform these
automated steps include by way of example, STARlet Manual Load, a
Modular Arm for 4/8/12 ch./MPH, 8 channels with 1000 .mu.l
Pipetting Channels and an iSWAP Plate Handler, all available from
Hamilton Science Robotics. If centerfuging is needed or desired, an
Agilent VSpin Microplate Centerfuge can be used. The software may
be Celigo API Software. The incubator may be a Cytomat Incubator.
For plate handling a Cytomat 24 Barcode Reader, Cytomat 23 mm
Stackers, and a Cytomat 400 mm transfer station may be used. For
plate tilting, one may use a MultiFlex Tilt Module. The system
controller may be a Dell PG with a Windows XP operating system. The
carrier package may be a Q Growth Carrier Package.
[0118] System 1, Part B: Quarantine Growth Workflow, Mycoplasma
Test [0119] 1. Retrieve from incubator to deck of Quarantine Growth
STARlet, remove media from wells to plate for ELISA based
mycoplasma test. [0120] 2. Manually transfer 96-well assay plates
to Quarantine Assay STARlet.
[0121] System 1, Part C: Quarantine Growth Workflow, after Passing
Mycoplasma Testing [0122] 1. Expanded fibroblasts distributed into
multiple cryovials, capped, transferred to SAM -80.degree. C.
[0123] The system components that may be used to perform these
automated steps may be selected from the same components used in
the Quarantine Growth Workflow, except a STARlet Auto Load may be
used. A Spectramax L Reader may be used as a spectral acquisition
device.
[0124] System 2: Quarantine Assay Workflow [0125] 1. Test using
glow luminescence method, Lonza MycoAlert. [0126] 2. Perform
luminescence plate read on spectral acquisition device.
[0127] The system components that may be used to perform these
automated steps include STARlet Manual Load, a Modular Arm for
4/8/12 ch./MPH, 8 channels with 1000 .mu.l Pipetting Channels and
an iSWAP Plate Handler, all available from Hamilton Science
Robotics. For luminescence assays the BioTek Synergy HT Reader may
be used. The system controller may be a Dell PG with a Windows XP
operating system. The carrier package may be a Q Growth Carrier
Package.
[0128] Systems 3, 4, and 5: Thawing, Infection and
Identification
[0129] Thawing Module & Infection Module [0130] 1. Retrieve
cryotubes from SAM -80.degree. C. (61, 190) [0131] 2. Thaw on
warming block (122) [0132] 3. Decap (Hamilton Capper Decapper)
(126) [0133] 4. Add media to dilute cryoprotectants (122) [0134] 5.
Spin (128) [0135] 6. Resuspend in plating data (122) [0136] 7.
Plate one sample per well of 6-well (62, 122) [0137] 8. Move to
incubator (130, 132) [0138] 9. Fibroblasts recover for about 3-4
days [0139] 10. Confluence check on Cyntellect Celigo Cytometer
(124) [0140] 11. Fibroblast passaging of all wells on the same day
for reprogramming (122) [0141] 12. In batches, tryspin passage
wells (122) [0142] 13. Count cells on Cyntellect Celigo Cytometer
(124) [0143] 14. Plate a defined number per well on one-to-three
wells of a 24-well plate consolidating samples onto as few as
24-well plates as possible (64, 122) [0144] 15. Return plates to
the incubator overnight (130, 132) [0145] 16. Retrieve plates and
thaw virus in tube format and add to each well of the fibroblasts
in the 24-well plates (130, 122) [0146] 17. Daily partial media
exchanges (122)
[0147] Magnetic Sorting Module [0148] 18. Harvest cultures with
accutase to single-cell suspension (134) [0149] 19. Dilute in
staining buffer (134) [0150] 20. Stain with magnetic beads against
fibroblast surface marker (134) [0151] 21. Wash step (134) [0152]
22. Apply to magnet (for Dynal beads) or column (for Miltenyi
system) (134, 136) [0153] 23. Retrieve non-magnetic fraction to new
wells (134) [0154] 24. Count cells on Cyntellect Celigo Cytometer
(124) [0155] 25. Dilute to appropriate cell density for delivering
1-10 cells per well to 96-well plate in passaging media (66, 134)
[0156] 26. Retrieve new Matrigel or matrix-coated 96-well plate
from 4.degree. C. incubator (142) [0157] 27. Distribute cells to
96-well matrix plates, number based on cell count for example, two
per plates per infection (66, 134) [0158] 28. Return plates to
incubator (132) [0159] 29. Daily partial media exchanges (122)
[0160] Colony Identification Module [0161] 30. Retrieve 96-well
plates from incubator to Colony identification liquid handler (66,
132, 138) [0162] 31. Perform live cell stain with pluripotency
surface marker (138) [0163] 32. Image on Cyntellect Celigo
Cytometer (140) [0164] 33. Identify wells with a single-marker
positive colony that has a sharp colony border (140) [0165] 34.
Techs review hits and select 6 per original sample for passage and
retrieve plate and positive well IDs. [0166] 35. Cherry-pick wells
with single positive colonies (138) [0167] 36. Retrieve new
Matrigel or matrix coated 96-well plate from 4.degree. C. incubator
(68, 142) [0168] 37. Harvest selected wells and passage to new
96-well matrix plate consolidating clones onto as few plates as
possible and plating each in passaging media (68, 138) [0169] 38.
Daily partial media exchanges (122)
[0170] The system components that may be used to perform these
automated steps may be selected from the same components used in
the Quarantine Growth Workflow with the addition of one or more
CORE 96 PROBEHEAD II 1000 .mu.l model probe heads.
Systems 6, 7, and 8: Maintenance, QC, Expansion, and Freezing
[0171] Maintenance Module [0172] 39. Will serially-passage clones
1:1 into new 96-well matrix-coated plates until colony density is
high enough (68-72, 160) [0173] 40. Daily feeding of all plates
with .about.75% media exchange with 96-tip head (160) [0174] 41.
Periodic monitoring of colony density and growth rates on
Cyntellect Celigo Cytometer (166) [0175] 42. Plate replication to
produce plates for QC of clones (74-86, 160) [0176] 43. Goal is to
expand clones onto multiple plates for use in several QC assays to
eliminate poorly-performing clones until left with two-to-three
high-quality clones per original sample [0177] 44. Will also
cherry-pick and re-array clones that pass QC steps as the poor
clones are eliminated to consolidate clones onto as few plates as
possible (80, 86, 160) [0178] 45. Daily feeding throughout this
process (160)
[0179] QC Module [0180] 46. Harvest cells (74, 150) [0181] 47.
Count cells (164) [0182] 48. Plate a defined cell number in
V-bottom plates (range of 5000-10000 cells/well) in 2-6 replicates
per line (84, 150) [0183] 49. Return to incubator--(1 g
aggregation) (172) [0184] 50. Media exchange after two days (150)
[0185] 51. Incubate for additional 12 days in incubator (172)
[0186] 52. Partial media exchange every two days (150) [0187] 53.
Transfer to nucleic acid prep station to remove media from wells
leaving embryoid bodies in the well (84, 192) [0188] 54. Resuspend
in RNA lysis buffer and combine and mix replicates for each sample
and make plates available for analysis in Nanostring nCounter assay
(84, 192)
[0189] Freezing Module [0190] 55. Begins with a 96-well plate after
an expansion passage (88) [0191] 56. Incubate 6 days in incubator
(172) [0192] 57. Partial media exchange every day (154) [0193] 58.
Remove plate from incubator (88, 162) [0194] 59. Remove media
(needs to be complete) (154) [0195] 60. Add cool Pre-freeze media
(diluted matrigel in growth media) (154) [0196] 61. Incubate in
incubator for 1 h (172) [0197] 62. Remove media (needs to be
complete) (154) [0198] 63. Addition of cold freezing media--low
volume (154) [0199] 64. Seal plate (88, 164 [0200] 65. Samples
taken off-line to -80.degree. C. storage to freeze (190) [0201] 66.
Store in vapor phase Liquid Nitrogen
[0202] Cryovial Storage [0203] 67. Begins with a 96-well plate
after an expansion passage (90) [0204] 68. Incubate 6 days (172)
[0205] 69. Daily partial media exchanges (154) [0206] 70. Passage
wells 1:1 to a 24-well plate (92, 154) [0207] 71. Incubate 6 days
(172) [0208] 72. Daily partial media exchanges (154) [0209] 73.
Passage wells 1:1 to a 6-well plate (94, 154) [0210] 74. Incubate
4-6 days (172) [0211] 75. Daily partial media exchanges (154)
[0212] 76. Remove plate from incubator (162) [0213] 77. Partial
media exchange with pre-freeze media (154) [0214] 78. Incubate in
incubator for 1 h (172) [0215] 79. Harvest cells for freezing as
for normal passage (154) [0216] 80. Move to matrix tubes,
two-to-three tubes per well (96, 154) [0217] 81. Spin and remove
media (168, 154) [0218] 82. Addition of cold freezing media (154)
[0219] 83. Cap tubes (170) [0220] 84. Samples taken off-line to
-80.degree. C. storage (190)
[0221] The system components that may be used to perform these
automated steps may be selected from the same components used in
the Quarantine Growth Workflow.
[0222] The iPSCs of the present invention may be differentiated
into a number of different cell types to treat a variety of
disorders by methods known in the art. For example, iPSCs may be
induced to differentiate into hematopoetic stem cells, muscle
cells, cardiac muscle cells, liver cells, cartilage cells,
epithelial cells, urinary tract cells, neuronal cells, and the
like. The differentiated cells may then be transplanted back into
the patient's body to prevent or treat a condition or used to
advance medical research or in to develop drug discovery assays.
Thus, the methods of the present invention may be used to as a
treatment or to develop a treatment for a subject having a
myocardial infarction, congestive heart failure, stroke, ischemia,
peripheral vascular disease, alcoholic liver disease, cirrhosis,
Parkinson's disease, Alzheimer's disease, diabetes, cancer,
arthritis, wound healing, immunodeficiency, aplastic anemia,
anemia, Huntington's disease, amyotrophic lateral sclerosis (ALS),
lysosomal storage diseases, multiple sclerosis, spinal cord
injuries, genetic disorders, and similar diseases, where an
increase or replacement of a particular cell type/tissue or
cellular de-differentiation is desirable.
[0223] In one embodiment, the inventive system can also be used to
obtain cell populations enriched in fully reprogrammed cells, from
among cells that have undergone differentiation in established iPSC
cell lines that were cultured under both murine embryonic
fibroblast (MEF) feeder layer, as well as feeder reconditions. The
inventive system further enables the live-sorting of defined
subpopulations of fully-reprogrammed, or differentiated, iPSC cells
into 96-well plates for use in high-throughput screening
campaigns.
[0224] FIG. 1 shows the steps performed by System 1, including
plating of a biopsy (2), outgrowth and passaging (4) (rolling
production on liquid handling robot), QC (6) (automated testing for
mycoplasma), and (8) automated freezing on liquid handling
robot.
[0225] FIG. 2 shows the steps performed by Systems 2, 3, and 4.
Fibroblasts are plated by the automated system (10), reprogramming
factors are introduced by the automated system (12), iPSCs are
isolated by automated sorting and isolation (14), desired clones
are selected and expanded by the automated system (16), automated
quality checks (QC) for pluripotent status by marker assays and
embryoid body assays (18), followed by automated freezing and
storage of desired cells (20).
[0226] FIG. 3 is a flowchart showing the step (22) through (60)
involved in System 1.
[0227] FIG. 3 illustrates an example of the workflow and decision
tree for production of fibroblasts from biopsies. The workflow is
divided into Quarantine (58) and Clean phases (60). As biopsies
enter the facility, a technician plates biopsies in 6-well plates
(22) and logs the plates into the automated incubator (24). After
biopsies are given time to attach to the plate, the liquid handling
robot retrieves the plates from the automated incubator to feed and
check confluency of the outgrowths on an automated microscope (26).
The plates are returned to the incubator and allowed to outgrow
(28). The liquid handler removes the plate from the incubator and
exchanges the media for antibiotic and antimycotic free media (30).
The robot moves the plate to the incubator for another five days
(32). The robot then removes the plate and retrieves media to
daughter plates for mycoplasma test (34). The daughter plates are
moved to the Quarantine Assay system for mycoplasma testing (36). A
choice is then made based on a positive signal from the assay (38).
If all wells of a 6-well plate fail with a positive mycoplasma
assay result (40) they are discarded. If all wells of a 6-well
plate are negative and free of mycoplasma, they are transferred out
of quarantine into the clean growth system (46). If some wells are
positive and some wells are negative, the negative wells are
maintained in quarantine (42). The negative wells are passaged (44)
to new plates, transferred to the incubator, and the source plates
containing positive wells are discarded. These cultures proceed
through steps to retest for mycoplasma (24, 26, 28, 30, 32, 34, 36,
38). Clean cultures are monitored for growth (50), passaged (52)
and frozen in cryovials (54, 56).
[0228] FIGS. 4A, 4B1, 4B2, and 4C illustrate an example of the flow
of patient samples through multi-well tissue culture plates during
the automated reprogramming process. At the top of each diagram, a
flowchart describes the flow of procedures performed at each step
of the workflow (70, 88, 98). At the bottom of each diagram,
multi-well cell culture plates are shown with platemaps for example
samples represented by shaded wells or groups of wells marked with
sample labels (61-68, 72-86, 88-96). Transfer of a sample from
plate-to-plate or well-to-well through the procedure is shown from
left to right as indicated by arrows. As shown in FIG. 4A, the
automated iPSC derivation process begins when patient samples and
control fibroblast samples (61) are plated in individual wells of a
6-well plate (62). These are passaged at defined cell number into
individual wells of a 24-well plate (64) for infection using
viruses encoding reprogramming factors or other means of
introducing reprogramming factors to the cells. In the next step,
reprogrammed samples are depleted of non-reprogrammed cells by cell
sorting or, as is preferred, using magnetic bead based enrichment
and plated at clonal density in multiple wells in 96-well plates
(66). Two such plates are shown in this example. In this example, 6
wells, as indicated by wells with a dot in the middle (66) are
identified containing a single clone positive for a pluripotency
surface marker as assayed by immunofluorescent analysis on
automated imager. These clones are passaged and cherry picked to
reformat the clones into a minimum number of 96-well plates (68).
The example figure shows six clones per individual starting sample
and indicates that clones from 16 starting sample can be arrayed
onto a 96-well plate. To facilitate plate processing, this cherry
picking step can be performed over multiple passages to consolidate
the clones onto a minimum number of plates. As show in FIGS. 4B1
and 4B2, these clones are serially passaged until confluence of
stem cell colonies within a well is achieved for each starting
sample (72). Each plates' samples are then replicated onto
duplicate plates (74-86), to allow for the quality control (6) and
selection of clones that demonstrate appropriate stem cell
characteristics. To begin the QC process, one plate is generated by
the system for a Pluripotency quality control assay needed to
determine pluripotent status of the individual clones (74) and one
plate is generated for carrying forward in subsequent passages
(76). The plate that is carried forward is passaged again into
three plates (78, 80, 82) for further quality control and
expansion. One plate is harvested for QC assays to characterize
Karyotype and genetic diversity (78). A second plate (82) is
passaged onto v-bottom plates to form embryoid bodies (84) for a QC
assay that assesses differentiation capability of the iPS clones.
The final plate (80) is carried forward for further expansion.
Individual clones that do not pass quality control from previous
pluripotency QC assays are not carried forward as shown by the "X"
in the wells indicated in FIG. 4. In the example shown in FIG. 4B2,
the consolidated plate (86) will contain iPS lines (or
differentiated lines) from up to 32 individuals represented by 3
iPS clones per individual on a single 96 well plate or up to 96
individuals if represented by a single clone each. Remaining clones
are consolidated onto as few plates as possible until one to three
clones remain (86-92). As shown in FIG. 4C, these are expanded for
cryopreservation while attached to the plate (88) or further
expanded (92-94) and cryopreserved in cryovials (96). Any or all
information from the pluripotency marker screen shown in FIG. 4A
(70), and the quality control assays shown in FIG. 4B1 can be used
alone or in combination to decide which clones to select for
consolidation and arraying in the automated process.
[0229] Methods for transfecting and transforming or reprogramming
adult cells to form iPSC lines are generally known, e.g., Takahashi
et al., 2007 Cell, 131: 861-872, 2007, Yu et al., 2007, Science,
vol. 318, pp. 1917-1920. iPSC are induced from somatic cells with
reprogramming factors. Reprogramming factors are contemplated to
include, e.g., transcription factors. The method for reprogramming
adult cells includes, e.g., introducing and expressing a
combination of specific transcription factors, e.g., a combination
of Oct3/4, Sox2, Klf4 and c-Myc genes. Others have demonstrated
that other transcription factors may be employed in transforming or
reprogramming adult cells. These other transcription factors
include, e.g., Lin28, Nanog, hTert and SV40 large T antigen as
described, for example, by Takahashi et al., 2006 Cell, 126:
663-676 and Huiqun Yin, et al. 2009, Front. Agric. China 3(2):
199-208, incorporated by reference herein.
[0230] In another aspect, iPSCs can be generated using direct
introduction of RNAs into a cell, which, when translated, provide a
desired protein or proteins. Higher eukaryotic cells have evolved
cellular defenses against foreign, "non-self," RNA that ultimately
result in the global inhibition of cellular protein synthesis,
resulting in cellular toxicity. This response involves, in part,
the production of Type I or Type II interferons, and is generally
referred to as the "interferon response" or the "cellular innate
immune response." The cellular defenses normally recognize
synthetic RNAs as foreign, and induce this cellular innate immune
response. In certain aspects where the ability to achieve sustained
or repeated expression of an exogenously directed protein using RNA
is hampered by the induction of this innate immune response, it is
desirable to use synthetic RNAs that are modified in a manner that
avoids or reduces the response. Avoidance or reduction of the
innate immune response permit sustained expression from exogenously
introduced RNA necessary, for example, to modify the developmental
phenotype of a cell. In one aspect, sustained expression is
achieved by repeated introduction of synthetic, modified RNAs into
a target cell or its progeny. The inventive methods include natural
or synthetic RNAs.
[0231] The natural, modified, or synthetic RNAs in one aspect, can
be introduced to a cell in order to induce exogenous expression of
a protein of interest in a cell. The ability to direct exogenous
expression of a protein of interest using the modified, synthetic
RNAs described herein is useful, for example, in the treatment of
disorders caused by an endogenous genetic defect in a cell or
organism that impairs or prevents the ability of that cell or
organism to produce the protein of interest. Accordingly, in some
embodiments, compositions and methods comprising the RNAs described
herein can be used for the purposes of gene therapy.
[0232] The RNAs described can advantageously be used in the
alteration of cellular fates and/or developmental potential. The
ability to express a protein from an exogenous RNA permits either
the alteration or reversal of the developmental potential of a
cell, i.e., the reprogramming of the cell, and the directed
differentiation of a cell to a more differentiated phenotype. A
critical aspect in altering the developmental potential of a cell
is the requirement for sustained and prolonged expression of one or
more developmental potential altering factors in the cell or its
immediate progeny. Traditionally, such sustained expression has
been achieved by introducing DNA or viral vectors to a cell. These
approaches have limited therapeutic utility due to the potential
for insertional mutagenesis.
[0233] One of the areas that can most benefit from the ability to
express a desired protein or proteins over a sustained period of
time from exogenous RNAs as described herein is the generation of
pluripotent or multipotent cells from cells initially having a more
differentiated phenotype. In this aspect, RNAs encoding a
reprogramming factor or factors are used to reprogram cells to a
less differentiated phenotype, i.e., having a greater developmental
potential.
[0234] A major goal of stem cell technology is to make the stem
cell differentiate into a desired cell type, i.e., directed
differentiation or produce cells via transdifferentiation. Not only
are the compositions and methods described herein useful for
reprogramming cells, they are also applicable to this directed
differentiation and transdifferentiation of cells to a desired
phenotype. That is, the same technology described herein for
reprogramming is directly applicable to the differentiation of the
reprogrammed cell, or any other stem cell or precursor cell, for
that matter, to a desired cell type.
[0235] In some embodiments of this aspect and all such aspects
described herein, the synthetic, modified RNA molecule comprises at
least two modified nucleosides. In one such embodiment, the two
modified nucleosides are selected from the group consisting of
5-methylcytidine (5mC), N6-methyladenosine (m6A),
3,2'-O-dimethyluridine (m4U), 2-thiouridine (s2U), 2'
fluorouridine, pseudouridine, 2'-O-methyluridine (Um), 2' deoxy
uridine (2' dU), 4-thiouridine (s4U), 5-methyluridine (m5U),
2'-O-methyladenosine (m6A), N6,2'-O-dimethyladenosine (m6Am),
N6,N6,2'-O-trimethyladenosine (m62Am), 2'-O-methylcytidine (Cm),
7-methylguanosine (m7G), 2'-O-methylguanosine (Gm),
N2,7-dimethylguanosine (m2,7G), N2,N2,7-trimethylguanosine
(m2,2,7G), and inosine (I). In one such embodiment of this aspect
and all such aspects described herein, the at least two modified
nucleosides are 5-methylcytidine (5mC) and pseudouridine. (see
e.g., Rossi US 2012/0046346, herein incorporated by reference).
[0236] Genes, proteins or RNA used in the methods of the invention
include but are not limited to OCT4, SOX1, SOX 2, SOX 3, SOX15, SOX
18, NANOG, KLF1, KLF 2, KLF 4, KLF 5, NR5A2, c-MYC, 1-MYC, n-MYC,
REM2, TERT, and LIN28.
[0237] It has also been shown that a single transcription factor
may be employed in reprogramming adult fibroblasts to iPSCs with
the addition of certain small molecule pathway inhibitors. Such
pathway inhibitors include e.g., the transforming growth
factor-beta (TGFb) pathway inhibitors, SB431542
(4-[4-(1,3-benzodioxol-5-yl)-5-(2-pyridinyl)-1H-imidazol-2-yl]-benzamide)-
, and A-83-01
[3-(6-Methyl-2-pyridinyl)-N-phenyl-4-(4-quinolinyl)-1H-pyrazole-1-carboth-
ioamide], the extracellular signal-regulated kinases (ERK) and
microtubule-associated protein kinase (MAPK/ERK) pathway inhibitor
PD0325901
(N-[(2R)-2,3-dihydroxypropoxy]-3,4-difluoro-2-[(2-fluoro-4-iodo-
phenyl)amino]-benzamide), the GSK3 inhibitor CHIR99021
[6-((2-((4-(2,4-Dichlorophenyl)-5-(4-methyl-1H-imidazol-2-yl)pyrimidin-2--
yl)amino)ethyl)amino)nicotinonitrile] which activates Wnt signaling
by stabilizing beta-catenin, the lysine-specific demethylase1
Parnate (a/k/a tranylcypromine), the small molecule activator of
3'-phosphoinositide-dependent kinase-1 (PDK1) PS48
[(2Z)-5-(4-Chlorophenyl)-3-phenyl-2-pentenoic acid], the histone
deacetylase (HDAC) inhibitors sodium butyrate and valproic acid,
small molecules that modulate mitochondrial oxidation (e.g.,
2,4-dinitrophenol), glycolytic metabolism (fructose
2,6-bisphosphate and oxalate), HIF pathway activation
(N-oxaloylglycine and Quercetin) Zhu et al., 2010, Cell Stem Cell
7: 651-655, incorporated by reference herein it its entirety. Zhu
et al showed that Oct4 combined with Parnate and CHIR99021 was
sufficient to reprogram adult human epidermal keratinocytes.
[0238] Although individual protocols differ, a general
reprogramming protocol consists of expanding differentiated adult
cells from tissue samples, e.g., skin biopsies and contacting them
with reprogramming factors as discussed above, e.g., infecting
them, i.e., transfecting, with e.g., expression vectors, such as
viral constructs containing transcripts for pluripotent
transcription factors. The fibroblasts are obtained by art-known
methods, e.g., by mechanically disrupting the tissue followed by
enzymatic dissociation to release the fibroblasts, and culturing
the fibroblasts by art-known methods, e.g., as described by Dimos
et. al., 2008, Science Vol. 321 (5893): 1218-1221.
[0239] While illustrative aspects of the invention use vectors,
e.g., viral vectors, plasmid vectors, in some aspects vectors are
not required for transfection techniques, including those
transferring mRNA molecules to cells.
[0240] Transfection of the fibroblasts with an expression vector is
carried out according to instructions provided with the desired
vector. After a time (e.g., ranging from about 2 to about 10 days
post-transfection, the cells are dissociated and contacted with
fluorescent tagged antibodies raised against the CD13.sup.NEG,
SSEA4.sup.POS and Tra-1-60.sup.POS surface markers. The dissociated
and antibody-labeled cells are then resuspended in a phosphate
buffered saline solution and moved to an automated sorting and
isolation of iPSC clones. Surface marker positive cells are sorted
by tag color or absence thereof directly into sterile tubes
containing tissue culture media or multi-well (6-96 well) tissue
culture plates coated with MEFs or cell free biological matrices
and cultured until formation of visible colonies occurs.
[0241] Colonies are then further confirmed as iPSC by light
microscopic inspection of the resulting clones or optionally by
microscopic fluorescence inspection of clones labeled with
fluorescent tagged antibodies. Optionally, in certain embodiments,
one or more of the vectors also insert a green fluorescence protein
(GFP) expression marker, for convenience in sorting and
identification. Several individual colonies possessing
morphological characteristics consistent with pluripotent ES cell
lines are plucked from cultures and expanded individually to form
monoclonal cultures.
[0242] In some embodiments of the present invention cells are
subjected to analysis to provide early confirmation and
identification of iPSCs. Preferably, such analysis is conducted by
Southern blot, or other art-known methods which include, but are
not limited, to MicroArray, NanoString, quantitative real time PCR
(qPCR), whole genome sequencing, immunofluorescence microscopy,
flow cytometry, and fluorescence activated cell sorting.
[0243] In one embodiment detection of enzymatic activity of
alkaline phosphatase, positive expression of the cell membrane
surface markers SSEA3, SSEA4, Tra-1-60, Tra-1-81 and the expression
of the KLF4, Oct3/4, Nanog, Sox2 transcription factors in, for
example, presumptively reprogrammed human fibroblasts, confirms
that a clone is an iPSC. In one embodiment all of the markers are
present, but in some embodiments a subset of the markers are
present.
[0244] In another embodiment positive expression of the cell
membrane surface markers SSEA4 and Tra-1-60 and negative expression
of CD13 provides an improved method for identifying reprogrammed
human fibroblasts and confirming that a clone is an iPSC. This
improved system is described in more detail in Example 3, whereby
fluorescence activated cell sorting (FACS) is used to identify and
isolate cells/clones that are CD13-negative, SSEA4-positive and
Tra-1-60-positive resulting in improved yield/selection of
reprogrammed IPSCs and depletion of both parental and contaminating
partially reprogrammed cells.
[0245] In some aspects the present invention provides "gene sets"
comprising genes whose expression can be used to detect, or confirm
the presence or generation of, particular cells such as iPSCs or
other pluripotent cells or differentiated cells derived from such
iPSCs or other pluripotent cells. Such gene sets, and methods and
compositions (such as probes and/or other detection agents) that
allow detection of the expression of genes from such gene sets, can
be used in a variety of different situations. For example they can
be used in accordance with the automated systems described herein
(for example as part of a colony identification step or a quality
control step), or they can be used in any other situation in which
it is desired to detect, or confirm the presence or generation of
pluripotent stem cells, such as iPSCs, or differentiated cells
produced therefrom.
[0246] In one embodiment the present invention provides the
"Pluri25" gene set, and nucleic acid probes or other agents (such
as antibodies) capable of detecting expression of genes in the
Pluri25 gene set (which may be referred to as a Pluri25 probe set).
Such a gene/probe set may be used to detect, or confirm the
presence or generation of, iPSCs. The Pluri25 gene/probe set
comprises the following genes, or probes or other agents for
detection of the expression of the following genes: four retrovial
transgenes (tOct4, tSox2, tKlf4, and tC-Myc), four Sendai
transgenes (tOct4, tSox2, tKlf4, tC-Myc) plus Sendai vector marker
(SeV), seven pluripotency markers (POU5F1 (Oct4), SOX2, KLF4, MYC,
LIN28, NANOG, and ZFP42), three spontaneous differentiation markers
(SOX17, AFP, and NR2F2), one fibroblast marker (ANPEP (CD13)),
three house-keeping markers (ACTB, POLR2A, and ALAS1) and two sex
markers (SRY and XIST)--for a total of 25 markers. The genes in the
Pluri25 gene set are also listed in Table 1, below:
TABLE-US-00001 TABLE 1 Pluri25 Gene Set Retro- Sendai Pluripotency
Spontaneous Fibro- House- viral transgenes Markers Differentiation
blasts keeping tOct4 S-tOct4 POU5F1 SOX17 ANPEP ACTB (OCT4) (CD13)
tSox2 S-tKlf4 SOX2 AFP POLR2A tKlf4 S-tC-myc KLF4 NR2F2 ALAS1
tC-Myc S-tSox2 MYC SeV LIN28 NANOG ZFP42
[0247] A Pluri25 probe set may comprise nucleic acid probes or
other agents (such as antibodies) capable of detecting expression
or expression products of each of the genes in the Pluri25 gene
set. Individual probes or detection agents may be used for each
gene or, where appropriate, single probes or detection agents
spanning several of the genes or gene expression products may be
used. For example, a single nucleic acid probe spanning all of the
four retroviral transgenes may be used. The sequences of each of
the genes in the Pluri25 gene set are known in the art, and nucleic
acid probes or other detection agents (such as antibodies) capable
of detecting expression of each of these genes may be available in
the art or may be made using standard methods known in the art. The
Pluri25 gene set or probe set can be used to monitor pluripotency
in human stem cell cultures, analyze contamination with
differentiated cells or human fibroblasts, monitoring the sex of
the cells, and monitor expression of retroviral and/or Sendai
transgenes or vector components. The Pluri25 gene or probe set also
contains a probe (SeV) for monitoring Sendai virus expression
independent of expression of any transgenes. Further description of
the Pluri25 gene/probe set, including validation studies and other
data generated using the Pluri25 gene/probe set, is provided in
Example 3, and Table 1.
[0248] In some embodiments variations on the Pluri25 gene or probe
set may be used. For example, in some embodiments the Pluri25 gene
or probe set may be modified so as to exclude the retroviral
transgene markers but keep the Sendai transgene and/or Sendai
vector markers. In other embodiments, the Pluri25 gene or probe set
may be modified so as to exclude the Sendai transgene and/or Sendai
vector markers but keep the retrovial transgene markers. In other
embodiments the Pluri25 gene or probe set may be modified so as to
exclude both the Sendai transgene/vector markers and the retrovial
transgene markers. Thus, in one embodiment, the present invention
provides a gene or probe set comprising: seven pluripotency markers
(POU5F1 (Oct4), SOX2, KLF4, MYC, LIN28, NANOG, and ZFP42), three
spontaneous differentiation markers (SOX17, AFP, and NR2F2), one
fibroblast marker (ANPEP (CD13)), three house-keeping markers
(ACTB, POLR2A, and ALAS1) and two sex markers (SRY and XIST)--for a
total of 16 markers.
[0249] In another embodiment the "3GLSC100" gene set, and in
particular nucleic acid probes or other agents (such as antibodies)
capable of detecting expression products of genes in the 3GLSC100
gene set (which may be referred to as a 3GLSC100 probe set) may be
used to detect, or confirm the presence or generation of iPSCs
(similarly to the Pluri25 gene set) and can also be used to monitor
differentiation of pluripotent stem cells by embryoid body assays
(either directed or undirected) and can be used in accordance with
the analysis methods described by Bock et al. (2011) "Reference
Maps of human ES and iPS cell variation enable high-throughput
characterization of pluripotent cell lines," Cell 144: 439-452, the
contents of which are hereby incorporated by reference. The
3GLSC100 gene set comprises 83 genes selected from among the
published germlayer scorecard of Bock et al. and 17 additional
genes that are a subset of the Pluri25 gene set. The genes in the
3GLSC100 gene set are listed in Table 2 below.
TABLE-US-00002 TABLE 2 3GLSC100Gene Set Mesoderm Ectoderm Endoderm
Retroviral Sendai Pluripotent Other Housekeeping ABCG2 ABCG2 APOE
tOct4 tOct4 POU5F1 SRY ACTB ADIPOQ APOE CD44 tSox2 tSox2 NANOG XIST
POLR2A ANPEP CD44 CDH2 tKlf4 tKlf4 ZFP42 ALAS1 CD34 CDH2 CDX2
tC-Myc tC-Myc CD36 CRABP2 CTNNB1 SeV CD4 EN1 FOXA2 CD44 FAS GATA4
CDH1 FGFR2 GATA6 CDH2 FUT4 GCG CDH5 GATA2 HNF1A CEACAM1 GATA3 HNF1B
DLL1 HAND1 ISL1 FUT4 ICAM1 ITGA6 GATA3 ITGA4 ITGB1 GATA4 ITGA6
NEUROG3 HHEX ITGB1 NKX2-5 ICAM1 MAP2 PAX6 INHBA MAPT PDX1 ITGA4
MCAM SLC2A2 ITGA6 MNX1 SST ITGAL NCAM1 SYP ITGAM NEFL THY1 ITGAV
NES ITGAX NEUROG3 ITGB1 NGFR ITGB3 NOG KDR NOTCH1 KIT OTX2 LEF1
PAX3 MCAM PAX6 MME PAX7 MYOD1 PDGFRA MYOG SNAI2 NCAM1 SOX10 NES
SOX2 NGFR SOX9 NOTCH1 SYP PECAM1 TDGF1 SDC1 TH SPI1 THY1 SRF STAT3
T THY1 TNFRSF1A TWIST1
[0250] A 3GLSC100 probe set may comprise nucleic acid probes or
other agents (such as antibodies) capable of detecting expression
or expression products of each of the genes in the 3GLSC100 gene
set. Individual probes or detection agents may be used for each
gene or, where appropriate, single probes or detection agents
spanning several of the genes or gene expression products may be
used. For example, a single nucleic acid probe spanning all of the
four retroviral transgenes in the 3GLSC100 gene set may be used.
The sequences of each of the genes in the 3GLSC100 gene set are
known in the art, and nucleic acid probes or other detection agents
(such as antibodies) capable of detecting expression of each of
these genes may be available in the art or may be made using
standard methods known in the art. The 3GLSC100 gene set or probe
set can be used in the same ways that the Pluri25 gene set is used
and can also be used (as described above). Further description of
the 3GLSC100 gene/probe set, including validation studies and other
data generated using the 3GLSC100 gene/probe set, is provided in
Example 3.
[0251] In some embodiments variations on the 3GLSC100 gene or probe
set may be used. For example, in some embodiments the 3GLSC100 gene
or probe set may be modified so as to exclude the retroviral
transgene markers but keep the Sendai transgene and/or Sendai
vector markers. In other embodiments, the 3GLSC100 gene or probe
set may be modified so as to exclude the Sendai transgene and/or
Sendai vector markers but keep the retrovial transgene markers. In
other embodiments the 3GLSC100 gene or probe set may be modified so
as to exclude both the Sendai transgene/vector markers and the
retrovial transgene markers.
[0252] In another embodiment the "cardiac 1" or "cardiac 2" gene
set (collectively the "cardiac gene sets"), and in particular
nucleic acid probes or other agents (such as antibodies) capable of
detecting expression products of genes in such gene sets (which may
be referred to as a cardiac probe sets) may be used to detect, or
confirm the presence or generation of, cells that are on a path
towards differentiation into cardiomyocytes, such as cells that are
have been derived from iPSCs or other pluiropotent cells and have
been treated to encourage differentiation down a cardiomyocyte
lineage. The "cardiac 1" gene set comprises the following genes:
ACTN1, BMP4, GATA4, GJA1, IRX-4, ISL1, KDR, MEF2A, MEF2C, MESP1,
MYH6, MYH7, MYL2, MYL7, NKX2-5, NPPA, PDGFRa, SIRPA, TBX20, TBX5,
TNNI3, TNNT2, VCAM1, VWF, MIXL1, NANOG, OCT4, SOX17, Brachury T and
KCNJ2--for a total of 30 genes. The "cardiac 2" gene set comprises
the all of the genes in the cardiac 1 gene set and the following
four additional genes: GAPDH, GUSB, HPRT1, and TBP--for a total of
34 genes.
[0253] A cardiac probe set may comprise nucleic acid probes or
other agents (such as antibodies) capable of detecting expression
or expression products of each of the genes in the cardiac gene
set. Individual probes or detection agents may be used for each
gene or, where appropriate, single probes or detection agents
spanning several of the genes or gene expression products may be
used. The sequences of each of the genes in the cardiac gene set
are known in the art, and nucleic acid probes or other detection
agents (such as antibodies) capable of detecting expression of each
of these genes may be available in the art or may be made using
standard methods known in the art.
[0254] The cardiac gene sets or probe sets can be used to establish
the differentiation stage of pluripotent stem cells when pushed to
differentiate towards a cardiomyocyte phenotype. The cardiac gene
sets comprise pluripotency markers, cardiac mesoderm markers,
cardiac progenitor markers, immature cardiomyocyte markers, and
mature cardiomyocyte markers. They also include vascular markers
and surface markers expressed by cardiomyocytes during
differentiation to facilitate purification, for example by via flow
cytometry or by a method using magnetic beads. In some embodiments
variations on the cardiac 1 and cardiac 2 gene or probe sets may be
used.
[0255] Any art-known transfection vector may be employed as a
reprogramming factor, including, e.g., an RNA such as mRNA,
microRNA, siRNA, antisense RNA and combinations thereof. Other
expression vectors that may be employed include, e.g., a
retrovirus, a lentivirus, an adenovirus, an adeno associated virus,
a herpes virus, a Sindbis virus, a pox virus, a bacula virus, a
bacterial phage, a Sendai virus and combinations thereof.
Preferably, an employed vector is a non-replicative vector such as,
e.g., Sendai virus vectors engineered to be nonreplicative. The
preferred Sendai virus vector, while incapable of replication,
remains capable of productive expression of nucleic acids encoding
protein(s) carried by the vector, thereby preventing any potential
uncontrolled spread to other cells or within the body of a
vaccinee. This type of Sendai vector is commercially available as a
CytoTune.TM.-iPSC Sendai viral vector kit (DNAVEC, DV-0301).
[0256] Any art-known transfection method may be employed to insert
such vectors into the adult fibroblasts, including, e.g.,
electroporation, gene gun, and the like. Chemical transfection is
optionally conducted by means of a transfecting agent e.g., a
polymer, calcium phosphate, a cationic lipid, e.g., for
lipofection, and the like. Cell penetrating peptides are also
optionally employed to carry vectors or other agents into the adult
fibroblast cells. In brief, cell-penetrating peptides include those
derived from proteins, e.g., protein transduction domains and/or
amphipathic peptides that can carry vectors or other agents into
the cell include peptides. The subject of cell-penetrating peptides
has been reviewed, e.g., by Heitz et al., 2009 British Journal of
Pharmacology, 157: 195-206, incorporated by reference herein in its
entirety. Other cell penetrating peptides are art-known, and are
disclosed by Heitz, Id. Other cell-penetrating technologies
including, e.g., liposomes and nanoparticles, are also contemplated
to be employed in the methods of the present invention. Liposomes
and nanoparticles are also described by Heitz, Id.
[0257] Antibodies can be employed in order to identify the
transformed cells. Four antibodies against stem cell specific
surface proteins are commonly used to identify and characterize
human pluripotent stem cell populations; SSEA3, SSEA4, Tra-1-60 and
Tra-1-81. The Stage Specific Embryonic Antigens 3 and 4 (SSEA3 and
SSEA4) are two monoclonal antibodies which recognize sequential
regions of a ganglioside present on human 2102Ep cells (Henderson
et al., 2002 Stem Cells 20: 329-337; Kannagi et al., 1983, Embo J
2: 2355-2361). The Tra-1-60 and Tra-1-81 antibodies were originally
raised against human embryonal carcinoma (EC) cells (P W et al.,
1984, Hybridoma 3: 347-361) and have been shown to specifically
recognize a carbohydrate epitope on a keratan sulfated glycoprotein
identified as podocalyxin, a member of the CD34-related family of
sialomucins (Badcock et al., 1999, Cancer Research 59: 4715-4719;
Nielsen et al., 2007, PLoS ONE 2: e237; Schopperle and DeWolf,
2007, Stem Cells 25: 723-730). Several other surface markers have
been shown to be expressed on ES cells and include CD326 or EpCam
(Sundberg et al., 2009, Stem Cell Res 2: 113-124), CD24 (Heat
Stable Antigen) and CD133 (Barraud et al., 2007, Journal of
Neuroscience Research 85, 250-259) (Gang et al., 2007, Blood 109:
1743-1751). Chan et al., 2009, Id. reported that the identification
of bona fide IPSc from fibroblasts undergoing reprogramming via
four factor retro viral transduction can be achieved via live cell
imaging and by the observation, over time, that fibroblasts lose
expression of the cell surface markers CD13 and D7Fib, and gain
expression of the pluripotent stem cell markers SSEA4 and Tra-1-60
(Chan et al., 2009, Id.).
[0258] Also contemplated to be within the scope of the invention
are compositions comprising iPSCs, e.g., compositions employed as
research tools, or as pharmaceutical compositions, comprising
effective amounts of iPSCs prepared by the inventive automated
system.
[0259] The invention further relates to treating a disease or
disorder in an animal or person in need thereof by administering
the iPSCs, e.g., methods of treatment and/or tissue/organ repair by
administering iPSCs produced by the inventive automated system, or
differentiated cells derived therefrom. Appropriate differentiated
cells (of ectodermal, mesodermal or endodermal lineage) may be
derived from iPSCs produced by the inventive methods. The mode of
administration can be determined by a person of skill in the art
depending on the type of organ/injury to be treated. For example,
iPSCs or differentiated cells derived therefrom, may be
administered by injection (as a suspension) or implanted on a
biodegradable matrix.
[0260] In addition, the invention relates to methods of testing
pharmaceuticals by contacting iPSCs, transdifferentiated, or
differentiated cells derived therefrom, for example, with one or
more pharmaceutical agents of interest, and then detecting the
effect of the applied pharmaceutical agent(s) on the contacted
cells. For efficiency, pharmaceutical agent(s) are applied to a
battery of iPSCs, or differentiated cells derived therefrom. The
cells can vary in tissue source, in differentiated cell type, or
allelic source, to allow identification of cells or tissue types
that react favorably or unfavorably to one or more pharmaceutical
agents of interest.
[0261] Further, the iPSCs produced by the inventive automated
system may be used as a vehicle for introducing genes to correct
genetic defects, such as osteogenesis imperfecta, diabetes
mellitus, neurodegenerative diseases such as, for instance,
Alzheimer's disease, Parkinson's disease, the various motor neuron
diseases (MND), e.g., amyotrophic lateral sclerosis (ALS), primary
lateral sclerosis (PLS), progressive muscular atrophy (PMA) and the
like.
[0262] iPSCs produced by the inventive automated system may also be
employed to provide specific cell types for biomedical research, as
well as directly, or as precursors, to produce specific cell types
for cell-based assays, e.g., for cell toxicity studies (to
determine the effect of test compounds on cell toxicity), to
determine teratogenic or carcinogenic effects of test compounds by
treating the cells with the compound and observing and/or recording
the compound's effects on the cells, e.g. effect on cellular
differentiation.
[0263] The present invention may be better understood by reference
to the following non-limiting Examples. The following examples are
presented in order to more fully illustrate the preferred
embodiments of the invention. They should in no way be construed,
however, as limiting the broad scope of the invention.
EXAMPLES
Example 1
Illustrative Automated Systems
[0264] FIG. 5A, 5B, 5C illustrate an example of the equipment
configuration needed to accomplish the workflow. FIG. 5A shows a
system configuration for the automated expansion and quality
control of a fibroblast bank. FIG. 5B shows a system configuration
for the automated thawing of patient samples, such as fibroblasts,
automated introduction of reprogramming factors with the patient
samples, such as fibroblasts, automated cell sorting with
MultiMACS, and automated colony identification and reformatting.
FIG. 5C shows a system configuration for the automated expansion of
iPS clones, automated Embryoid Body production, and automated
freezing.
Automated Derivation of a Fibroblast Cell Bank
[0265] As an example, the hardware configuration used to accomplish
the derivation of a fibroblast bank consists of a Hamilton STARlet
liquid handling robot (100) connected to the following hardware
components: a Cytomat 24C GLS automated incubator (108) that allows
for the incubation of cell cultures, a Cyntellect Celigo cytometer
(102) for automated image acquisition and analysis, an Agilent
V-Spin automated centrifuge (106) for the centrifugation of cells
in plates or tubes, and a Hamilton Capper DeCapper (104) for the
automated capping and decapping of cryotubes. These components are
further controlled by programmable software (118) on a PC that
communicates with all instruments and controls the manipulation of
cell culture-ware and cells among the hardware components. The
controller software further communicates with scheduling software
(120) to link System interactions. The Hamilton STARlet (100) is
equipped with a Modular Arm for 4/8/12 channel pipetting, 8
pipetting channels, iSWAP plate handler, CO-RE Gripper for plate
and lid handling, MultiFlex tilt Module for tilting plates during
media exchanges, Hamilton Heated Shaker 2.0, as well as a Carrier
Package for flexible layout of the liquid handling platform with
plate and lid parks, pipette stackers, daughter plate stackers and
troughs for holding media. The Cyntellect Celigo (102) is comprised
of an imaging unit and programmable software on a PC for control of
image acquisition and image analysis. The Celigo is preferred
because it does not move the cell culture plates during imaging
thereby reducing agitation of plated biopsies. The Hamilton Capper
Decapper (104) and the Agilent V-Spin centrifuge (106) are
contained with the Hamilton STARlet within a NuAire BSL II
biosafety cabinet (110) to maintain a sterile operating environment
during manipulation of cell culture plates.
[0266] To control plate handling on the automated system, MICROLAB
STAR VENUS TWO Base Pack 4.3 software (118) with VENUS Dynamic
Scheduler 5.1 (120) are used in conjunction with individual
attached hardware component drivers for the centrifuge (106),
Capper Decapper (104), Celigo (102), and Cytomat 24 (108) and
Cytomat transfer station to integrate the operation of the system.
The following methods programmed using the provided controller
software (118) are needed for functionality of the system and can
be combined in defined sequence to accomplish the derivation of
fibroblast lines from patient skin biopsies: [0267] 1. Load 6-well
biopsy plates (22, 24) onto the STARlet (100) and transfer to the
Cytomat incubator (108). [0268] 2. Confluency check (26, 28) on
Celigo (102) and a media exchange on the STARlet (100). [0269] 3.
Confluency check (28) on Celigo (102). [0270] 4. Media change (30)
on the STARlet (100) for full media exchange. [0271] 5. Assay plate
preparation (34) on STARlet (100) and Agilent V-Spin centrifuge
(106). [0272] 6. Passaging (44) on the STARlet (100). [0273] 7.
Passage and cherry pick (42) on the STARlet (100). [0274] 8.
Passage, harvest and freeze on the STARlet (100). [0275] 9.
Retrieve plates (46, 40) onto the STARlet (100) from the Cytomat
(108).
Automated Mycoplasma Testing on Quarantine Assay System
[0276] An independent hardware configuration is used to accomplish
the mycoplasma testing of a fibroblast bank and consists of a
Hamilton STARlet liquid handling robot (112) connected to a BioTek
Synergy HT Reader (114). These components are further controlled by
programmable software (116) on a PC that communicates with all
instruments and controls the manipulation of cell culture-ware and
cells between the hardware components. The Hamilton STARlet (112)
is equipped with a Modular Arm for 4/8/12 channel pipetting, 8
pipetting channels, iSWAP plate handler, CO-RE Gripper for plate
and lid handling, as well as a Carrier Package for flexible layout
of the liquid handling platform with plate and lid parks, pipette
stackers, daughter plate stackers and plate parks and troughs for
holding reagents needed for the assay.
[0277] To control plate handling on the automated system, MICROLAB
STAR VENUS TWO Base Pack 4.3 software (116) is used in conjunction
with the attached hardware component drivers for the BioTek Synergy
HT Reader (114) to integrate the operation of the system. A method
is programmed using this software that allows execution of the
MycoAlert Mycoplasma Detection assay (36) and data analysis to
determine assay result (38).
Automated System for Thawing, Infection, and Identification of
Reprogrammed Cells
[0278] The hardware configuration needed to thaw fibroblasts,
infect fibroblasts with reprogramming viruses, magnetic sort of
reprogrammed cells, and identification of stem cell colonies is
composed of three Hamilton STAR liquid handling units (122, 136,
138), two Cytomat 48C incubators (132), one Cytomat 2C 425
incubator (142), two Cyntellect Celigo cytometers (124, 140),
Hamilton Capper DeCapper (126), Agilent V-Spin (128), Miltenyi
MultiMACS magnetic separation device (136). The liquid handlers, a
Celigo, the Hamilton Capper Decapper and Agilent V-Spin are all
connected by a Hamilton Rack Runner robotic rail (130). Each
Hamilton STAR is equipped with a Modular Arm for 4/8/12 channel
pipetting, 8 pipetting channels, iSWAP plate handler, CO-RE Gripper
for plate and lid handling, one or more MultiFlex tilt Module for
tilting plates during media exchanges, one or more Hamilton Heated
Shaker 2.0, as well as carrier packages for flexible layout of the
liquid handling platform with plate and lid parks, pipette
stackers, daughter plate stackers and troughs for holding media.
One of the Hamilton STAR liquid handlers (122) is also equipped
with a 96-well pipetting head. One Celigo (140) and the Cytomat 2C
incubator (142) are connected directly to one of the Hamilton STARs
(138) to facilitate automated cell sorting. The Hamilton STARs are
contained within NuAire BSL II biosafety cabinets (144, 146,148) to
maintain a sterile operating environment during manipulation of
cell culture plates. The remaining components are enclosed in a
Hepa filtered hood to maintain a sterile operating environment
during transportation of cell culture plates among the devices. The
Cytomat 48C incubator (132) is connected to the other components of
the system by the Rack Runner transport rail (130).
[0279] To control plate handling on the automated system, MICROLAB
STAR VENUS TWO Base Pack 4.3 software controllers (150, 152, 154)
with VENUS Dynamic Scheduler 5.1 (156) are used in conjunction with
individual attached hardware component drivers for all of the
Hamilton STARs (122, 134, 138), the centrifuge (128), the
Capper/decapper (126), the two Celigos (140, 124), the Rack Runner
(130), and Cytomat 24 (132), the Cytomat 2C (142), and associated
Cytomat transfer stations to integrate the operation of the system.
The following methods programmed using the provided controller
software (150, 152, 154) are needed for functionality of the system
and can be combined in a defined sequence to accomplish derivation
of iPS colonies from fibroblasts: [0280] 1. Load mycoplasma free
6-well biopsy plates (48) onto the STAR (122) and transfer to the
Cytomat incubator (132) under clean growth conditions (60). [0281]
2. Confluency check (50) on Celigo (124) and a media exchange on
the STAR (122). [0282] 3. Passage, harvest (52) and freeze (54, 56)
on the STAR (122). [0283] 4. A thawing method whereby cryotubes
containing fibroblasts (61) are loaded and thawed on the STAR
(122), followed by decapping of tubes (126) and washing of
fibroblast, followed by resuspending cells in plating media and
plating fibroblasts on 6 well plates (62) and transferring to
Cytomat incubator (132). [0284] 5. Media change on the STARlet
(122) for full media exchange. [0285] 6. Confluency check on Celigo
(124). [0286] 7. Passaging and seeding of fibroblasts in 24-well
plates (64) on the STARlet (122). [0287] 8. A method for infection
of fibroblasts (64) on the STARlet (122). [0288] 9. A method to add
a defined volume of media to wells on STAR (122, 138, 144). [0289]
10. A method for executing a half media exchange on STAR (122, 138,
144). [0290] 11. A method for magnetic sorting, dilution and
plating (66) on the STAR (144) attached to the Miltenyi MultiMACS
(136) and Celigo (124). [0291] 12. A method for a three quarter
media exchange on the STAR (122, 138, 144). [0292] 13. A method for
a executing an immunocytochemical stain on live colonies followed
by automated imaging of the colonies (66) using a STAR (138) and
Celigo (140). [0293] 14. A method for harvesting, cherry picking
and replating colonies (68) from selected wells on a STAR (138).
[0294] 15. Retrieve plates onto the STARlet (122, 138, 144) from
the Cytomat (132).
Automated System for Expansion, Quality Control, and Freezing of
Reprogrammed Cells
[0295] The hardware configuration needed to expand reprogrammed
Stem Cell Colonies, generate plates of colonies for quality control
assays and generate plates and tubes for cryostorage is composed of
three Hamilton STAR liquid handling units (150, 154, 160), Cytomat
24C incubator (172), one Cytomat 2C 425 incubator (174), one
Cyntellect Celigo cytometer (166), Hamilton Capper DeCapper (170),
Agilent V-Spin (168), and Agilent PlateLoc plate sealer (164). The
liquid handlers, a Celigo, the Hamilton Capper Decapper, Agilent
V-Spin, and Agilent PlateLoc plate sealer are all connected by a
Hamilton Rack Runner robotic rail (162). The Hamilton STARs and
STARlet are equipped with Modular Arms for 4/8/12 channel
pipetting, 8 pipetting channels, iSWAP plate handlers, CO-RE
Grippers for plate and lid handling, one or more MultiFlex tilt
Modules for tilting plates during media exchanges, one or more
Hamilton Heated Shaker 2.0s, as well as a carrier packages for
flexible layout of the liquid handling platforms with plate and lid
parks, pipette stackers, daughter plate stackers and troughs for
holding media. One of the STARs (160) also has a 96 channel
Multichannel pipetting head to facilitate media exchanges and
passaging. The Cytomat 2C and Cytomat 24C incubators are connected
to the Hamilton STARs by a Hamilton Rack Runner transport rail
(162) to facilitate automated media exchanges. The Hamilton STARs
are contained within a NuAire BSL II biosafety cabinet (176, 178,
180) to maintain a sterile operating environment during
manipulation of cell culture plates. The remaining components are
enclosed in a Hepa filtered hood to maintain a sterile operating
environment during transportation of cell culture plates among the
devices.
[0296] To control plate handling on the automated system, MICROLAB
STAR VENUS TWO Base Pack 4.3 software controllers (182, 184, 186)
with VENUS Dynamic Scheduler 5.1 (188) are used in conjunction with
individual attached hardware component drivers for the centrifuge,
decapper, plate sealer, Celigo, and Cytomat incubators and Cytomat
transfer station to integrate the operation of the system. The
following methods are needed for functionality of the system and
can be combined in a defined sequence to expand cell cultures in
plates for quality control assays and freezing in plates or
cryovials: [0297] 1. A loading method on the STAR (160) to receive
plates (68) from the previous stage into the Cytomat incubator
(172). [0298] 2. Media change on the STAR (150, 154, 160) for full
media exchanges using tilt modules and 8-channel pipetting arms.
[0299] 3. Confluency check on Celigo (166) with associated methods
to transport plates to and from the STARs (150, 154, 160) and
Cytomat incubator (172). [0300] 4. A method for passaging and
seeding of iPSCs in 96-well plates (68-90) on the STARs (150, 154,
160). [0301] 5. A method for executing a partial media exchanges on
the STARs (150, 154, 160). [0302] 6. A method for harvesting,
cherry picking and replating colonies from selected 96-well wells
to new 96-well plates (80, 82, 86, 88) on a STAR (150, 154, 160).
[0303] 7. A method for harvesting, cherry picking and replating
colonies from selected 96-well wells to new 24-well plates (90, 92)
on a STAR (154). [0304] 8. A method for harvesting and cherry
picking and replating colonies from selected 24-well wells to new
6-well plates (92, 94) on a STAR (154). [0305] 9. Passage, harvest
and distribute cells in freezing plates (88) on the STAR (154).
[0306] 10. Passage, harvest and distribute cells in cryotubes (96)
on the STAR (154). [0307] 11. Retrieve plates onto the STARs (150,
154, 160) from the Cytomat 24C (172) or Cytomat 2C (174).
Example 2
Production of a Fibroblast Bank for Reprogramming
[0308] The first step in the workflow to derive iPSCs from patient
samples is to obtain and expand adult cells. This is accomplished,
for example, by obtaining a skin punch biopsy or discarded dermal
tissue, then isolating and expanding cultures of fibroblasts from
the tissue. In the workflow described in the present Example, this
is accomplished by the automated system comprised of Systems 1 and
2. The automated components of System 1 and 2 (100-120) and System
3 (122-132, 154, 190) perform the steps needed to derive a
fibroblast bank stored in cryotubes (61) from patient samples,
including plating of a patient biopsy (2, 22-24), outgrowth and
passaging (4, 26-32) (rolling production on liquid handling robot),
QC (6, 34-46) (automated testing for mycoplasma), and automated
freezing on the liquid handling robot (8, 48-56). For example, the
workflow and decision tree for production of fibroblasts from
biopsies is divided into Quarantine (58) and Clean phases (60). As
biopsies enter the facility, a technician plates biopsies in 6-well
plates (22) and logs the plates into the automated incubator (24)
to begin the quarantine workflow. After biopsies are given time to
attach to the plate, the liquid handling robot retrieves the plates
from the automated incubator to feed and check confluency of the
outgrowth of adult fibroblasts from the plated tissue on an
automated microscope (26). The plates are returned to the incubator
and allowed to continue to outgrow (28). The liquid handler removes
the plate from the incubator and exchanges the media for antibiotic
and antimycotic free media (30) to prepare for mycoplasma testing.
The robot moves the plate to the incubator for another five days
(32). The robot then removes the plate and retrieves media to
daughter plates for mycoplasma test (34). The daughter plates are
moved to the Quarantine Assay system for mycoplasma testing (36). A
choice is then made based on a positive signal from the assay (38).
If all wells of a 6-well plate fail with a positive assay result
(40) they are discarded. If all wells of a 6-well plate are
negative and free of mycoplasma, they are transferred out of
quarantine into the clean growth environment provided by Systems 3,
4, 5 (46). If some wells are positive and some wells are negative,
the negative wells are maintained in quarantine (42). The negative
wells are passaged (44) to new plates, transferred to the
incubator, and the source plates containing positive wells are
discarded. These cultures proceed through steps to retest for
mycoplasma (24-38). Clean cultures are monitored for growth (50),
passaged (52) and frozen in cryovials (54, 56, 61).
Production of Stem Cell Arrays
[0309] To produce iPSCs, Fibroblasts in cryotubes (61) are plated
by the automated system (10), reprogramming factors are introduced
by the automated system (12), iPSCs are isolated by automated
sorting and isolation in System (14), desired clones are selected
by the automated system (16), and expanded by the automated system
(16), automated quality checks by the automated system (QC) for
pluripotent status by marker assays and embryoid body assays (18),
followed by automated freezing and storage of desired cells by the
automated system (20). These steps are accomplished on the
automated systems 3, 4, 5, 6, 7, and 8 (122-192).
[0310] For example, the automated iPS derivation process begins
when 96 patient and control fibroblast samples in cryotubes (61)
are plated in individual wells of a 6-well plate (62). These are
passaged at defined cell number into individual wells of a 24-well
plate for infection using viruses encoding reprogramming factors
(64). In the next step, reprogrammed samples are depleted of
non-reprogrammed cells by cell sorting or magnetic bead-based
enrichment and plated at clonal density in multiple wells in
96-well plates (66). In this example, 6 wells (66) are identified
containing a single clone positive for a pluripotency surface
marker. These clones are cherry picked and consolidated into a
minimum number of 96-well plates (68). These clones are serially
passaged until confluence within a well is achieved for each
starting sample (72). Each plates' samples are then replicated onto
duplicate plates (74, 76), one plate for a Pluripotency quality
control assay needed to determine pluripotent status of the
individual clones (74) and one plate for carrying forward in
subsequent passages (76). The plate that is carried forward is
passaged again into three plates (78, 80, 82). One plate is
harvested for QC assay that assesses Karyotype and genetic
diversity (78), one plate (82) is passaged onto v-bottom plates to
form embryoid bodies (84) for a QC assay that assesses
differentiation capability of the iPS clones, and the final plate
(80) is carried forward for further expansion. Individual clones
that do not pass quality control from previous pluripotency QC
assays are not carried forward as indicated by "X" in the wells in
FIGS. 4B2 and 4C (80, 82, 90). Remaining clones are consolidated
onto as few plates as possible until one to three clones remain
(86). These clones are expanded for cryopreservation while attached
to the plate (88) or further expanded (92, 94) and cryopreserved in
cryovials (96).
[0311] Embryonic stem cells (ES) are also contemplated to be used
with the automated system of the invention to generate
differentiated adult cells. ES cells are derived from the
blastocyst of an early stage embryo and have the potential to
develop into endoderm, ectoderm, and mesoderm (the three germ
layers) (i.e., they are "pluripotent"). In vitro, ES cells tend to
spontaneously differentiate into various types of tissues, and the
control of their direction of differentiation can be challenging.
However, some progress has been achieved in the directed
differentiation of ES cells to particular types of differentiated
daughter cells. For example, it is now possible to direct the
differentiation of human ES cells to functional midbrain
dopaminergic neurons using defined factors added to the cell
cultures at defined stages of their stepwise differentiation (see,
e.g., Kriks et al., 2011 Nature, November 6. doi:
10.1038/nature10648 (Epub)). As differentiation is not homogenous,
it remains necessary to isolate populations of interest for further
study or manipulation. The process and instrumentation described
here could be used to first derive and expand pluripotent embryonic
stem cells and also isolate subpopulations of their differentiated
derivatives by automated methods including automated magnetic cell
isolation.
[0312] For example, whole human blastocysts can be plated on
matrices in multi-well plates amenable to the automated process.
Outgrowths from these plated blastocysts could be isolated using
the same automated magnetic isolation procedures performed by the
robotic instrumentation and methods described for the isolation of
induced pluripotent stem cells. The resulting human embryonic stem
cell lines could be expanded, selected by quality control assays
and frozen using the same automated procedures described
herein.
[0313] Further, using pluripotent stem cells, either blastocyst
derived or induced by defined factors or by somatic cell nuclear
transfer, differentiated derivatives can be isolated using the
described workflow and instrumentation. The differentiated
derivatives can be obtained by directed application of defined
factors required to induce a cell fate change or after spontaneous
differentiation. For example, inhibitors of the TGF beta pathway
can be used to induce neural cell fates from pluripotent stem
cells. Neural cells can be subsequently isolated from non-neural by
magnetic bead immunolabeling of surface antigens, such as NCAM. The
described workflow and instrumentation can be used to magnetically
isolate, select, culture and expand differentiated cells like
neurons. This process is also applicable to other differentiated
cell types, like cardiac cells, for which there exist antibodies
that recognize cell surface antigens specific to the cell type of
interest.
[0314] Multipotent stems cells are also contemplated to be used
with the automated systems of the invention to generate
differentiated adult cells. In particular, mesenchymal stem (MS)
cells can be employed to generate differentiated adult cells using
the automated systems of the invention. MS cells are the formative
pluripotent blast or embryonic-like cells found in bone marrow,
blood, dermis, and periosteum and placenta that are capable of
differentiating into specific types of mesenchymal or connective
tissues including adipose, osseous, cartilaginous, elastic,
muscular, and fibrous connective tissues. The specific
differentiation pathway which these cells enter depends upon
various influences from mechanical influences and/or endogenous
bioactive factors, such as growth factors, cytokines, and/or local
microenvironmental conditions established by host tissues. Examples
include differentiation of MS cells into differentiated cells with
the properties of chondrocytes for cartilage repair, e.g., see U.S.
Pat. No. 8,048,673.
Chromosomal Testing
[0315] In some aspects, the Nanostring nCounter Plex2 Assay Kit is
used to target the 400 genomic loci, often known to be invariant
among the population, allows for integrated molecular karyotype
analysis coupled with "fingerprint" tracking of cell line identity.
The molecular karyotype analysis utilizes an average of 8 probes
per chromosome arm to verify genomic stability during the course of
cell culture derivation and expansion of iPSC lines. Identity
analysis will also be performed on all lines based on 30 common
copy number variations (CNVs) of polymorphic loci, which allows for
unambiguous identification of individual genomes.
Pluripotency Analysis
[0316] In one aspect, surface marker staining is performed to show
that cells are positive for Tra-1-60 surface marker, which is
monitored e.g., with the Celigo automated imager. PSC lines must
show a significant level of the pluripotency genes. In one example,
a probe set of 100 gene makers (described below) was utilized that
includes the six markers for pluripotency (Oct4, Klf4, cMyc, Nanog,
Lin28, ZFP42, and Sox2). To perform this analysis a sample of cells
was lysed and RNA was harvested. The nCounter Plex2 Assay Kit was
used to analyze expression levels in multiple samples and hundreds
of gene targets simultaneously enabling the high-throughput
approach to PSC characterization. As the nCounter gene expression
assays are quantitative, selection criteria is based on expression
levels falling within a range relative to a control panel of
established hESC lines analyzed grown under identical conditions.
Lines that pass pluripotency gene expression criteria will be
further expanded and differentiated in vitro in embryoid body (EB)
assays.
EB Formation Gene Expression Assay
[0317] It has been shown that epigenetic and transcriptional
variation is common among human pluripotent cell lines and that
this variation can have significant impact on a cell line's
utility. In an illustrative example, the panels of gene markers
includes: 83 different gene markers selected from each of the 3
germ layers (83), 5 retrovirus transgene (4 factors with single
detection probe, 1 probe), 5 sendai transgenes (4 factors+vector
only, 5), Oct4, Klf4, cMyc, Nanog, Lin28, ZFP42 (pluripotency, Sox2
is in germlayer group, 6 probes), sex markers (SRY, XIST (2)--donor
sex must match or lines will be rejected), and housekeeping genes,
ACTB, POLR2A, ALAS1 (3 probes).
hPSC Line Expansion and Storage
Automated Expansion:
[0318] Cell lines are expanded through plating of the initial cells
into 2 separate wells of a 6-well plates then placing them within a
CO2 incubator and allowing them to grow up to a maximum of 95%
confluence.
Storage
[0319] The vials are first placed within the SAM -80 freezer to
perform the initial slow cool. This system has automated monitoring
of temperature and logs of time the system is accessed.
[0320] Next, the vials are placed in LN2 for long-term storage.
Quality control for monitoring is detailed later in this proposal.
Each vial is individually marked with a unique 2D barcode and
inventory is tracked within the LIMS.
hPSC Line Characterization
[0321] iPSC and EB gene expression analysis-Set of probes covering
lineage differentiation assay scorecard (100 genes) to monitor germ
layer differentiation in EB assays, pluripotency markers, sex
markers and transgene expression
Freeze-Thaw Analysis
[0322] Cells are counted following recovery and plated in one well
of a 6-well plate. Colonies are photographed on the first day of
appearance and then 5 days later, colonies must display a doubling
time no larger than 36 hours.
Surface Marker Analysis
[0323] Perform surface marker analysis using automated system using
high content imaging of Tra-1-60 staining using the Celigo
automated imager.
iPSC and EB Gene Expression Analysis
[0324] Pluripotency gene expression--iPSC clones must show a
significant level of the pluripotency genes. A probe set of 100
gene makers (described below) was used that includes the six
markers for pluripotency (Oct4, Klf4, cMyc, Nanog, Lin28, ZFP42,
and Sox2). To perform this analysis a sample of cells is lysed for
each of the selected clones and RNA is harvested. The nCounter
Plex2 Assay Kit was used to analyze expression levels in multiple
samples and hundreds of gene targets simultaneously enabling the
high-throughput approach to iPSC characterization. As the nCounter
gene expression assays are quantitative, selection criteria is
based on expression levels falling within a range relative to a
control panel of established hESC lines analyzed grown under
identical conditions. Selected clones that pass pluripotency gene
expression criteria will be further expanded and differentiated in
vitro in embryoid body assays.
[0325] EB formation gene expression assay--In order to firmly
establish the nature and magnitude of epigenetic variation that
exists among human pluripotent stem cell lines, three genomic
assays were applied to 20 established embryonic stem cell (ESC)
lines and 12 iPSC lines that were recently derived and functionally
characterized. As a step toward lowering the experimental burden of
comprehensive cell line characterization, and to improve the
accuracy over standard existing assays, all of the data from these
studies are combined using the three genomic assays into a
bioinformatics scorecard, which enables high-throughput prediction
of the quality and utility of any pluripotent cell line. This
scorecard was used to analyze gene expression data from the EBs
formed from each clone of the iPSC lines. To test differentiation
potential, the automated system was used to generate EBs in 96-well
v-bottom plates and ends in RNA harvest for Nanostring nCounter
Plex2 Assay Kit. The score card comprised 83 different gene markers
selected from each of the 3 germ layers (83), 5 retrovirus
transgenes (4 factors with single detection probe, 1 probe), 5
sendai transgenes (4 factors+vector only, 5), Oct4, Klf4, cMyc,
Nanog, Lin28, ZFP42 (pluripotency, Sox2 is in germlayer group, 6
probes), sex markers (SRY, XIST (2)), and housekeeping genes (ACTB,
POLR2A, ALAS1 (3 probes).
Karyotype and Identity Analysis
[0326] Prior to accepting a line and at the end of each expansion,
the Nanostring nCounter Plex2 Assay Kit was used to target the 400
genomic loci allowed for integrated molecular karyotype analysis
coupled with "fingerprint" tracking of cell line identity. The
molecular karyotype analysis utilizes an average of 8 probes per
chromosome arm to verify genomic stability during the course of
cell culture derivation and expansion of iPSC lines. The
"fingerprint" identity tracking analysis will rely on a
combinatorial signature based on 30 common copy number variations
(CNVs) of polymorphic loci, which allows for unambiguous
identification of individual genomes. Additionally to avoid
misidentification, tissue donors known to be relatives will not be
processed in the same batch, as it is theoretically possible they
will have similar CNVs. The data from the identity analysis will be
cross-referenced with the initial CNV data to ensure that the LIMS
system properly tracked all cell lines.
Freeze-Thaw Analysis
[0327] Freeze-Thaw Analysis: one vial is thawed after
cryopreservation. Cells are counted following recovery and plated
in one well of a 6-well plate. Cultures are observed daily.
Colonies are photographed on the first day of appearance and then 5
days later. Colonies must at least double in diameter within 5 days
after first observation.
Automated Biopsy Outgrowth Tracking
[0328] Using the invention system, one can track the outgrowth of
biopsies as well as other tissue sources by automated and traceable
image analysis. As shown in FIG. 6, images and growth rates are
tracked during the production process. In FIG. 6A, biopsies or
discarded tissue are plated in multiple wells of a 6-well dish and
maintained by an automated system that feeds, images, passages, and
freezes fibroblast outgrowths. Examples of the image analysis
interface is shown for a typical sample. A single plate is used per
donated sample to minimize cross contamination. (B) Cell numbers
are extrapolated from confluence measurements based on linear
regression from a standard curve generated independently. (C) An
example of cell counts for a typical biopsy outgrowth maintained on
the automated system. Extrapolated cell numbers per patient sample
are plotted for each well independently (top) allowing calculation
of total output from the sample (bottom).
[0329] FIG. 7 shows FACS analyses and graphs showing automated iPSC
reprogramming. Expression levels of pluripotent surface markers on
reprogrammed human fibroblasts were followed over a 3 week period
to observe reprogramming kinetics and determine optimal time points
at which to isolate defined cell populations. (A) FACS gating
scheme used for analysis. (B) A substantial proportion of cells
co-expressing traditional pluripotency surface markers SSEA4 &
TRA-1-60 retain the fibroblast marker CD13 at all timepoints during
reprogramming using either retroviral or Sendai vectors to
introduce reprogramming factors Oct4, Sox2, Klf4 and c-Myc. Box
plots indicating aggregated data from 131 experiments (Retrovirus,
n=66, Sendai virus, n=65) are shown. While Sendai mediated
reprogramming produces more SSEA4/TRA-1-60 double positive cells,
(C) there is a delay in elimination of CD13 from the surface. (D)
Example staining pattern of a patient cell line reprogrammed using
Sendai/Cytotune system on the automated system. At both 7 and 13
dpi, more than half of SSEA4/TRA-1-60 double positive cells have
lost CD13. Additionally, at both timepoints assayed, CD13
negative/Nanog positive cells are present in this fraction,
suggesting these can be isolated by negative selection against
CD13.
[0330] FIG. 8 shows FACs pre-sort analyses and a part of the
automated system to demonstrate enrichment and clone selection of
iPSCs. (A) Non-reprogrammed cell populations can be depleted from
cultures of iPSCs by negative selection by a fibroblast marker.
This strategy leaves iPSCs untouched. In the example, fibroblasts
are efficiently removed from the culture containing 2% established
iPSCs leaving TRA-1-60 positive iPSCs untouched. (B) A Miltenyi
MultiMACS system integrated into Hamilton liquid handler can sort
24 samples in parallel. (C) An example colony of newly derived
iPSCs derived by negative selection using anti-fibroblast antibody
conjugated magnetic beads on the MultiMACS system. Phase contrast,
nuclear stain by Sytox, surface marker stain by TRA-1-60 and
nuclear Nanog staining. (D) The iPS enriched fraction from the
anti-fibroblast magnetic negative selection step is plated on
96-well imaging plates at limiting dilution. These plates are
screened using live-cell staining for the pluripotency surface
marker TRA-1-60 or TRA-1-81. Wells with TRA-1-60 positive iPSCs are
identified by automated image analysis using the Celigo software
capable of single colony confirmation. Wells that meet both
criteria of containing a single colony that is positive for the
surface marker are selecting for passaging and expansion and QC.
(E) Colonies produced by automated Sendai infection of adult
fibroblasts.
[0331] iPSC induction has also been demonstrated by automated
transfection of modified mRNA. iPSC colonies from BJ fibroblasts
were efficiently recovered after 10 days of automated delivery of a
transfection mix containing modified mRNA. After an additional two
days culture, the same well was stained with TRA-1-60 to identify
undifferentiated cells. iPSCs in the well demonstrate that these
are undifferentiated iPSCs. iPSC colonies isolated by purification
away from non-reprogrammed cells using magnetic bead depletion on
the automated system were efficiently recovered.
[0332] High throughput scorecard assays for gene expression have
been generated. The first stage of a quality control screen uses a
panel of pluripotency differentiation and transgene markers to
choose an initial set of three clones. FIG. 9A shows transcript
counts after normalization to HK gene expression for two HESC
lines, Sendai positive control, fibroblast negative control, and
iPS lines derived by FACS sorting assayed at passage 5 and 10. All
assays are run relative to a panel of normal HESC and iPS lines
maintained under similar conditions. Not shown was an example image
of an Embryoid body generated on the system in 96-well V-bottom
plates. The arrow points to the EB. FIG. 9C illustrates the second
stage of a quality control screen uses an additional 83 germ
layer/lineage markers to monitor differentiation capability in
embryoid body assays. Single EBs are generated and pooled to
generate RNA for expression analysis of germ layer markers in the
embryoid body scorecard assay. Shown is a cluster dendrogram
analysis of gene expression in EBs collected from nine different
embryonic stem cells lines. After normalization, data generated
from direct lysis of six EBs compares favorably to data generated
from total RNA extracted and purified from EBs prepared from bulk
culture.
[0333] FIG. 10 demonstrates high throughput karyotyping of iPSCs
based on Nanostring nCounter assays for CNVs. FIG. 10A is an
example of the nCounter Karyotype assay on BC1 iPSCs; FIG. 10B is
an example of the nCounter Karyotype assay on 1016 fibroblasts with
partial gain and loss of chromosome arms. Comparison to Affymetrix
SNP 6.0 chip data demonstrating copy number gains on a portion of
the q arm of Chr1 (top track, 1q21.2-1q43) and loss of part of the
long arm of Chr6 (bottom track, 6q16.3-6q26).
Example 3
Improved Methods for Reprogramming Human Dermal Fibroblasts
[0334] The work described in the present Example, including the
associated figures, tables and drawings, was published by one or
more of the inventors of the present application and others. The
citation for the publication is Kahler et al. (2013) "Improved
Methods for Reprogramming Human Dermal Fibroblasts Using
Fluorescence Activated Cell Sorting," PLoS ONE 8(3): e59867,
published Mar. 29, 2013, and the entire contents of Kahler et al.
2013, including its figures, supplemental figures, and supplemental
tables, are incorporated herein by reference in their entirety.
[0335] Current methods to derive induced pluripotent stem cell
(iPSC) lines from human dermal fibroblasts by viral infection rely
on expensive and lengthy protocols. One major factor contributing
to the time required to derive lines is the ability of researchers
to identify fully reprogrammed unique candidate clones from a mixed
cell population containing transformed or partially reprogrammed
cells and fibroblasts at an early time point post infection.
Failure to select high quality colonies early in the derivation
process results in cell lines that require increased maintenance
and unreliable experimental outcomes. Here, an improved method is
described for the derivation of iPSC lines using fluorescence
activated cell sorting (FACS) to isolate single cells expressing
the cell surface marker signature CD13NEGSSEA4POSTra-1-60POS on day
7-10 after infection. This technique prospectively isolates fully
reprogrammed iPSCs, and depletes both parental and "contaminating"
partially reprogrammed fibroblasts, thereby substantially reducing
the time and reagents required to generate iPSC lines without the
use of defined small molecule cocktails. FACS derived iPSC lines
express common markers of pluripotency, and possess spontaneous
differentiation potential in vitro and in vivo. To demonstrate the
suitability of FACS for high-throughput iPSC generation, 228
individual iPSC lines were derived using either integrating
(retroviral) or non-integrating (Sendai virus) reprogramming
vectors and performed extensive characterization on a subset of
those lines. The iPSC lines used in this study were derived from 76
unique samples from a variety of tissue sources, including fresh or
frozen fibroblasts generated from biopsies harvested from healthy
or disease patients.
Introduction
[0336] The discovery that differentiated somatic cells could be
reprogrammed to an embryonic stem cell-like state by forced
expression of four transcription factors (Oct4, Klf4, Sox2, cMyc)
has revolutionized the stem cell field [1]. Reprogrammed, or
induced pluripotent stem cells (iPSCs), show remarkable
similarities to embryonic stem cells (ESCs) and hold great promise
for in vitro disease modeling, drug discovery, and therapeutic
interventions because they provide a potentially unlimited source
of differentiated cells from individuals with specific diseases
[2], [3], [4], [5], [6].
[0337] However, initial derivation of stable iPSC clones by viral
transduction of dermal fibroblasts is a slow (4-6 weeks) and
inefficient (<0.01% of total fibroblasts) process. Current
methods of identifying colonies of bona fide iPSCs early in the
reprogramming process (2-3 weeks post-infection) utilize light
microscopy and manual isolation of candidate colonies, which
requires training and expertise in advanced cell culture
techniques. To enable future clinical applications requiring de
novo iPSC derivation, there remains a need for standardized and
validated methods for identifying, isolating and purifying
reprogrammed cells.
[0338] Previous imaging studies based on tracking of cell-of-origin
suggest that early events occur during defined factor
reprogramming, including a change in cell proliferation rates and
morphology [7], downregulation of CD13, a marker of mesenchymal
cells including fibroblasts [8], as well as upregulation of the
cell surface markers of pluripotency SSEA4 and TRA-1-60 [9]. These
studies demonstrate that both partially and fully reprogrammed
iPSCs can be identified by combined use of surface expression of
multiple markers. Recently, a method of enriching reprogrammed
fibroblasts by fluorescence activated cell sorting (FACS) for cells
with dual expression of the pluripotency surface markers SSEA4 and
TRA-1-81 arising late during reprogramming was described [10].
While a step forward, this method relies heavily on the use of a
defined small molecule cocktail, and multiple rounds of sorting and
extensive screening to identify fully reprogrammed clones. This
suggests that pluripotency markers alone are not sufficient to
purify fully reprogrammed iPSCs. Additionally, it is likely that
the high variability among clones seen within this population is
compounded by the use of integrating vectors to deliver the
reprogramming factors. Here, results confirm that throughout the
reprogramming process a significant proportion of
SSEA4POSTra-1-60POS cells retain the fibroblast surface marker,
CD13. Through the use of negative selection against CD13, fully
reprogrammed iPSCs were purified from partially reprogrammed cells
and parental fibroblasts by FACS. This method removes contaminating
cells at an early stage and can be used with a variety of cell
populations including: cells reprogrammed with DNA-integrating or
non-integrating viruses; fibroblasts harvested from healthy or
specific disease patients. Using this method, 228 iPSC lines have
been generated and characterized from 76 fibroblast lines obtained
from multiple sources including fresh biopsies, frozen stocks, and
cell line repositories.
Materials and Methods
Fibroblast Cell Culture
[0339] Explants of 3-mm dermal biopsies were minced and placed in a
60-mm tissue culture dish under a sterile coverslip held down by
sterilized silicon grease. Fibroblast medium [Dulbecco's modified
Eagle's medium (DMEM), supplemented with 10% fetal bovine serum,
Glutamax.TM., and penicillin/streptomycin (Invitrogen, Carlsbad,
Calif.)] was added, and dishes incubated at 37.degree. C. in a
humidified 5% CO2 atmosphere with media exchange every 5 days.
Fibroblast outgrowths were harvested by trypsinization, expanded in
a T25 flask in fibroblast medium, and allowed to reach .about.90%
confluence prior to freezing or splitting for reprogramming as
described below. For reprogramming, fibroblasts were used within
the first three passages from biopsy or within one passage after a
thawing. All parent fibroblast and reprogrammed lines were
subjected to cytogenetic analysis (Cell Line Genetics) and for DNA
fingerprinting by short tandem repeat (STR) analysis.
Fibroblast Reprogramming
[0340] Fibroblasts were reprogrammed using high titer stocks of
vesicular stomatitis virus G (VSVG)-coated retroviruses containing
Oct4, Sox2, cMyc, and Klf4 (Harvard Gene Therapy Initiative at
Harvard Medical School) as previously described [12], or the
non-integrating CytoTune.TM.--Sendai viral vector kit (Life
Technologies, A13780). Fibroblasts reprogrammed with retroviruses
were infected at 1.times.104 cells/well in 1 ml of human ESC medium
(HUESM) [Knockout.TM. DMEM supplemented with 20% Knockout.TM. serum
replacement (Invitrogen), 10 ng/ml bFGF (Invitrogen), nonessential
amino acids (Invitrogen), (3-mercaptoethanol (Invitrogen),
L-glutamine, and penicillin/streptomycin (Invitrogen)]. The medium
was exchanged on day 2 to HUESM containing ALK5 inhibitor SB431542
(2 .mu.M; Stemgent), MEK inhibitor PD0325901 (0.5 .mu.M; Stemgent),
and ROCK inhibitor [13] Thiazovivin (0.5 .mu.M; Stemgent)] and
changed daily thereafter. For Sendai virus mediated reprogramming,
5.times.105 fibroblasts were infected in fibroblast medium at a
multiplicity of infection of 3 (MOI3) for two days with daily
(HUESM) media exchanges. At day 7-10 days post-infection by retro
or Sendai viral protocols, cells were subjected to FACS analysis or
passaged onto feeder cells by enzymatic dissociation using Dispase
(GIBCO) and/or Accutase (Sigma-Aldrich) then passaged onto
.gamma.-irradiated murine embryonic fibroblasts (MEFs; Globalstem)
or Matrigel.TM. (BD Biosciences) coated plates in HUESM at
2.times.103 cells/cm2.
Fluorescent Activated Cell Sorting of Reprogrammed Fibroblasts
[0341] Cells enzymatically harvested as described above were
filtered through a 35 .mu.m cell strainer (BD biosciences) to
obtain a single cell suspension prior to resuspension in 100 .mu.l
of a sterile iPSC staining buffer [DPBS containing 0.5% bovine
serum albumin fraction V (BSA; Invitrogen), 100 U/ml
penicillin/streptomycin (Invitrogen), 2 mM EDTA (Invitrogen), and
20 mM glucose (Sigma)]. A cocktail of fluorescence-conjugated
antibodies [1 .mu.each anti-CD13 (555394) anti-SSEA4 (560219) and
anti-Tra-1-60 (560173), obtained from BD, CA] was added to the
cells and incubated at room temperature (RT) for 15 minutes
shielded from light. Stained cells were washed once with iPSC
staining buffer and sorted immediately on a 5 laser BD Biosciences
ARIA-IIu.TM. SOU Cell Sorter using "gentle FACS" sorting conditions
based on the work of Pruszak et al. (100 .mu.m ceramic nozzle, 20
psi) [14]. Some experiments included antibodies against SSEA3 (BD,
560237), or CD326 (BD, 347200) in the cocktail to confirm the
pluripotent status of the reprogrammed cells. Target cell
populations were sorted directly onto MEF layers (ARIA plate holder
at 37.degree. C.) at between 2.times.103 and 5.times.104 cells/well
in a 6-well plate containing HUESM plus 20 .mu.M Y-27632 (ROCK
inhibitor; Calbiochem). Two days after sorting, the ROCK inhibitor
was removed from the medium and replaced with SB431542 (2 .mu.M),
PD0325901 (0.5 .mu.M), and Thiazovivin (0.5 .mu.M) [13] with daily
media exchange. Several individual colonies were picked 7-10 days
after sorting and expanded for characterization.
Quantitative RT-PCR
[0342] Total RNA was isolated from duplicate or triplicate cell
samples using the RNeasy kit (QIAGEN, 74136). cDNA synthesis was
performed on 1 .mu.g RNA with SuperScript.TM. III First-Strand
system (Invitrogen 18080-051) and oligo(dT) primers. The cDNA was
diluted to a final volume of 200 .mu.l and 1 .mu.l was added to 500
nM of the forward and reverse primers in a final volume of 10
.mu.per PCR reaction. Quantitative real-time PCR was performed
using the GoTaq.RTM. SYBR Green Master kit (Promega, A6001) and
Mx3000p QPCR system (Stratagene). Primer sequences are provided in
Table 3, below.
TABLE-US-00003 TABLE 3 Quantitative real-time PCR Primers (S1)
FORWARD PRIMER REVERSE PRIMER GENE 5'-3' 5'-3' Oct 4
CCCCAGGGCCCCATT GGCACAAACTCCAGG (endogenous) TTGGTACC TTTTC (SEQ ID
NO: 1) (SEQ ID NO: 2) Sox2 ACACTGCCCCTCTCA GGGTTTTCTCCATGC
(endogenous) CACAT TGTTTCT (SEQ ID NO: 3) (SEQ ID NO: 4) Klf4
ACCCACACAGGTGAG GTTGGGAACTTGACC (endogenous) AAACCTT ATGATTG (SEQ
ID NO: 5) (SEQ ID NO: 6) C-Myc AGCAGAGGAGCAAAA CCAAAGTCCAATTTG
(endogenous) GCTCATT AGGCAGT (SEQ ID NO: 7) (SEQ ID NO: 8) Oct4
CCCCAGGGCCCCATT AACCTACAGGTGGGG (transgene) TTGGTACC TCTTTCA (SEQ
ID NO: 9) (SEQ ID NO: 10) Sox2 ACACTGCCCCTCTCA AACCTACAGGTGGGG
(transgene) CACAT TCTTTCA (SEQ ID NO: 11) (SEQ ID NO: 12) Klf4
GACCACCTCGCCTTA AACCTACAGGTGGGG (transgene) CACAT TCTTTCA (SEQ ID
NO: 13) (SEQ ID NO: 14) C-Myc AGCAGAGGAGCAAAA AACCTACAGGTGGGG
(transgene) GCTCATT TCTTTCA (SEQ ID NO: 15) (SEQ ID NO: 16) B2M
TAGCTGTGCTCGGGC TCTCTGCTGGATGAC TACT GCG (SEQ ID NO: 17) (SEQ ID
NO: 18)
Southern Blotting
[0343] Probes for human Oct4, Sox2, and KLF4 were generated by PCR
using the digoxigenin (DIG) probe synthesis kit (Roche) and
Southern blotting was performed using DIG System detection reagents
(Roche). Genomic DNA was isolated from human ESCs, parent
fibroblast cells, and iPSCs using the Qiagen DNA Mini kit. DNA
samples (5-10 .mu.g) were digested overnight with BglII to generate
a single cut in the integrated viral backbone of each transgene,
and digests were resolved on a 0.8% agarose gel (without ethidium
bromide), which was then denatured with 0.5% NaOH and neutralized.
The gel was transferred to a nylon membrane by overnight capillary
transfer. Wet membranes were crosslinked with 120 mJ UV (HL-2000
Hybrilinker, UVP) and allowed to dry. Membranes were pre-hybridized
with DIG Easy Hyb buffer for at least 1 h at 55.degree. C., then
incubated with the appropriate probe overnight at 55.degree. C.
Membranes were washed thoroughly using the DIG Wash and Block kit,
blocked for at least 1 h, and incubated with anti-DIG antibody for
30 min. Membranes were then washed and treated with CDP-Star
reagent to detect DIG-incorporated bands. Blots were stripped and
re-probed according to the manufacturer's instructions. Probe
sequences are provided in Table 4, below.
TABLE-US-00004 TABLE 4 Southern Blot Primers (S2) FORWARD PRIMER
REVERSE PRIMER GENE 5'-3' 5'-3' Oct 4 GAGAAGGAGAAGCTG
GTGAAGTGAGGGCTC (endogenous) GAGCA CCATA (SEQ ID NO: 19) (SEQ ID
NO: 20) Sox2 AGAACCCCAAGATGC TGGAGTGGGAGGAAG (endogenous) ACAAC
AGGTA (SEQ ID NO: 21) (SEQ ID NO: 22) Klf4 ACCTGGCGAGTCTGA
TCTTCATGTGTAAGG (endogenous) CATGG CGAGGTGG (SEQ ID NO: 23) (SEQ ID
NO: 24)
NanoString nCounter Assay
[0344] Total RNA was isolated from each iPSC clone between passage
10 and 15 using the RNeasy kit (Qiagen). A 100-ng sample of RNA was
then profiled using the NanoString nCounter system (NanoString,
Seattle, Wash.) using one of two custom-designed codesets. The
pluripotency codeset contains 25 probes for detection of the Sendai
and retroviral transgenes, pluripotency and spontaneous
differentiation markers, and housekeeping genes (Table 5). The
lineage codeset is derived from a previous study [15] and contains
85 probes for the three germ layers in addition to probes for
retroviral and Sendai transgenes, and housekeeping genes (Table 6).
RNA from a retrovirus-positive or Sendai-positive control line, a
fibroblast line (1043), and two human ESC lines (HUES42 and Hues16)
was included in each run. Data were analyzed using the nSolver
Analysis Software v1.0 (NanoString) and plotted using Prism
(Graphpad Software, La Jolla, Calif.). Data quality control and
normalization to geometric mean for both internal positive
controls, and subsequently for housekeeping genes, was performed in
the nSolver analysis software.
TABLE-US-00005 TABLE 5 Pluripotency Codeset (S3) Retro- Sendai
Pluripotency Spontaneous Fibro- House- viral transgenes Markers
Differentiation blasts keeping tOct4 S-tOct4 POU5F1 SOX17 ANPEP
ACTB (OCT4) (CD13) tSox2 S-tKlf4 SOX2 AFP POLR2A tKlf4 S-tC-myc
KLF4 NR2F2 ALAS1 tC-Myc S-tSox2 MYC SeV LIN28 NANOG ZFP42
TABLE-US-00006 TABLE 6 Lineage Codeset (S4) Mesoderm Ectoderm
Endoderm Retroviral Sendai Pluripotent Other Housekeeping ABCG2
ABCG2 APOE tOct4 tOct4 POU5F1 SRY ACTB ADIPOQ APOE CD44 tSox2 tSox2
NANOG XIST POLR2A ANPEP CD44 CDH2 tKlf4 tKlf4 ZFP42 ALAS1 CD34 CDH2
CDX2 tC-Myc tC-Myc CD36 CRABP2 CTNNB1 SeV CD4 EN1 FOXA2 CD44 FAS
GATA4 CDH1 FGFR2 GATA6 CDH2 FUT4 GCG CDH5 GATA2 HNF1A CEACAM1 GATA3
HNF1B DLL1 HAND1 ISL1 FUT4 ICAM1 ITGA6 GATA3 ITGA4 ITGB1 GATA4
ITGA6 NEUROG3 HHEX ITGB1 NKX2-5 ICAM1 MAP2 PAX6 INHBA MAPT PDX1
ITGA4 MCAM SLC2A2 ITGA6 MNX1 SST ITGAL NCAM1 SYP ITGAM NEFL THY1
ITGAV NES ITGAX NEUROG3 ITGB1 NGFR ITGB3 NOG KDR NOTCH1 KIT OTX2
LEF1 PAX3 MCAM PAX6 MME PAX7 MYOD1 PDGFRA MYOG SNAI2 NCAM1 SOX10
NES SOX2 NGFR SOX9 NOTCH1 SYP PECAM1 TDGF1 SDC1 TH SPI1 THY1 SRF
STAT3 T THY1 TNFRSF1A TWIST1
Embryoid Body Formation
[0345] Embryoid bodies (EB) were formed by placing clumps of iPSCs
in 96-well non-tissue culture treated V-bottom plates (Evergreen
222-8031-01V) containing HUESM. After 5 weeks of culture, EBs were
harvested, fixed in 4% paraformaldehyde (PFA) for 30 min at RT and
processed in 15% and 30% sucrose solutions for one day each prior
embedding in O.C.T., freezing, sectioning into 10 .mu.m slices and
mounting on glass slides. EB sections were immunostained with
antibodies against the markers shown in Table 7, below. Briefly, EB
sections were incubated with blocking solution 10% donkey serum in
PBST (PBS with 0.1% Triton-100) for 1 h at RT, followed by an
overnight incubation at 4.degree. C. with primary antibodies. After
washing three times with PBST, sections were incubated for 1 h at
RT with appropriate secondary antibodies obtained from Molecular
Probes. Finally, sections were washed and counterstained with DAPI
(1:1000 in PBS) for 15 min at RT.
TABLE-US-00007 TABLE 7 Primary Antibodies for Immunofluorescence
(S5) Antibody Company Catalog # Dilution Oct4 Stemgent 09-0023
1:250 Sox2 Stemgent 09-0024 1:250 Tra-1-60 Millipore MAB4381 1:250
SSEA4 R&D Systems MAB1435 1:250 Nanog R&D Systems AF1997
1:250 SSEA3 R&D Systems MAB1434 1:250 Smooth Muscle DAKO
M085101 1:500 Alpha-1-Fetoprotein DAKO A0502 1:500 TUJ1 Covance
MMS-435P 1:500 Nestin Millipore AB5922 1:500 MAP2 Abcam ab32454
1:500
Teratoma Assay
[0346] Manually (1023_C) and FACS-derived (1023_D2) cells were
dissociated using Dispase (Gibco 17105-041) for 15 minutes at
37.degree. C. to produce small clumps containing approximately
100-200 iPSCs/clump. The clumps were suspended in 100 .mu.l of
HUESM containing 100 .mu.Matrigel.TM. (BD Biosciences) and injected
subcutaneously into NOD-SCID I12rg-null mice (Jackson Laboratory)
following an intraperitoneal injection of carprofen (Pfizer) at 5
mg/kg. Teratomas were allowed to grow for 6-8 weeks, isolated by
dissection and fixed in 4% PFA overnight at 4.degree. C. Fixed
tissues were embedded in paraffin, sectioned at 10 .mu.m and
stained with hematoxylin and eosin (H&E).
Results
[0347] FACS Derivation of iPSCs
[0348] Previous studies have demonstrated downregulation of the
human fibroblast marker CD13 [8], and upregulation of the
pluripotency markers SSEA4 and TRA-1-60 occurs during reprogramming
[9]. These studies suggest that isolation of fully reprogrammed
iPSCs during early stages of reprogramming may be accomplished by
FACS using a combination of positive and negative surface markers.
While current sorting strategies for purification of pluripotent
cells rely on positive selection[7], it is possible that a
significant proportion of clones isolated using this method may not
be fully reprogrammed. To test this hypothesis, first the
conditions for survival of live-cell sorted, fully reprogrammed
cells was optimized by examining the expression levels of three
surface markers in a manually derived, early passage clone (p4) of
an iPSC line (1018) cultured on MEFs.
[0349] Populations of cells expressing all three markers were found
in the culture suggesting a heterogeneous mixture of cells
containing parental and partially reprogrammed fibroblasts FIG.
11A. Then the CD13NEGSSEA4POSTra-1-60POS (Tra-1-60POS) population
was sorted and, as a control, the CD13NEGSSEA4POSTra-1-60NEG
(Tra-1-60NEG) population was sorted to approximately 70% purity
directly into one well of a 6 well plate containing MEFs in the
presence of ROCK inhibitor Y-27632. The sorted populations were
maintained for 20 days on MEFs without ROCK inhibitor or removal of
differentiated cells or splitting prior to reanalysis by flow
cytometry (FCM). At 20 days post-sorting (dps), the cultures
originating from the enriched Tra-1-60POS population contained
fewer Tra-1-60NEG differentiated cells and no detectable CD13POS
parental fibroblasts. The Tra-1-60POS population was present in
these cultures at approximately double the proportion found in the
Tra-1-60NEG enriched culture (30% vs. 14%). Conversely, at 20 dps
the culture originating from the Tra-1-60NEG enriched population
contained a Tra-1-60POS population at a similar proportion to the
originally sorted culture (18% T vs. 14% T). However, these
cultures also contained a higher proportion of differentiated or
transformed cells (CD13NEGSSEA4NEGTra-1-60NEG) as well as adult
fibroblasts (CD13POS) suggesting that these FACS conditions allow
for purification of fully reprogrammed cells from contaminating
cell types.
[0350] To confirm this strategy, adult skin fibroblasts at 8 days
post infection (dpi) were sorted based on the
CD13NEGSSEA4POSTra-1-60POS surface marker profile. As a control,
the CD13NEGSSEA4POS population that contained two subpopulations of
cells expressing either Tra-1-60POS or Tra-1-60NEG was isolated in
parallel. 5,000 or 10,000 cells from each population were sorted
directly into MEF-containing plates, and monitored for the
formation of colonies. Small but distinct colonies were evident in
both sorted populations as early as 3 days post sort (dps), with
the CD13NEGSSEA4POSTra-1-60POS population producing larger and more
abundant colonies than the CD13NEGSSEA4POS population (3 dps, 11
dpi; FIG. 11B). Following an additional 2 weeks of expansion
without manual removal of differentiated cells, wells containing
the CD13NEGSSEA4POS population had become overgrown with
transformed and differentiated cells, whereas wells containing the
sorted CD13NEGSSEA4POSTra-1-60POS cells contained large,
well-separated colonies with few differentiated cells between the
colonies and lacked cells with transformed morphology (17 dps, 25
dpi; FIG. 11B). A 3-4 fold increase was observed in the number of
colonies present in wells containing the sorted
CD13NEGSSEA4POSTra-1-60POS cells compared to the sorted
CD13NEGSSEA4POS cells FIG. 11C.
[0351] CD13 expression was then analyzed within the
SSEA4POSTra-1-60POS population of reprogrammed fibroblasts at 7
dpi. Roughly one quarter of the SSEA4POSTra-1-60POS population
expressed CD13 indicating the presence of a heterogeneous
population of fully reprogrammed, transformed, or transitioning
cells (23% CD13POS, 66% CD13--; FIG. 11D), some of which expressed
both Nanog and CD13 FIG. 11E.
[0352] Because surface marker expression during reprogramming is
dynamic, the earliest time point was first identified at which to
enrich fully reprogrammed iPSCs. Time course analysis conducted by
flow cytometry following retroviral reprogramming suggested that
SSEA4POSTra-1-60POS cells were detectable as early as 7 dpi, and
their proportion increased up to 21 dpi, then remained constant as
marker negative cells outgrew the reprogrammed cells Table 3. The
SSEA4POSTra-1-60POS population also expressed the SSEA3 and CD326
pluripotency markers [16], [17], [18], [19]. SSEA4POSCD13POS cells
appeared by 7 dpi and while most of this population disappeared by
14 dpi, a proportion remained in the culture. To test whether this
timing was consistent among different skin samples, cultures
derived from a foreskin fibroblast line (0825), a healthy adult
control fibroblast line (1023), and a fibroblast line from a
subject with type I diabetes (1018) were analyzed for up to 21 dpi.
The three fibroblast cell lines showed a consistent emergence of
pluripotent surface markers with SSEA4POSTra-1-60POS cells present
at low numbers at 7 dpi (D7, 0.3%-0.4% FIG. 12A), increasing in
proportion at 14 dpi (D14, 1.4%-2.2%), and decreasing by day 21 as
other cells overtook the culture (D21, 0.7%), suggesting a
consistent appearance of potentially early reprogrammed cells
between 7 and 14 dpi. However, at early time points, the majority
of SSEA4POSTra-1-60POS cells also expressed CD13 (D7, 98%-100%).
The proportion of CD13POSSSEA4POSTra-1-60POS decreased
approximately half by day 14 post infection (D14, 37%-54%),
suggesting loss of this fibroblast marker on cells undergoing
reprogramming. Interestingly, the CD13POSSSEA4POSTra-1-60POS
population increased again by day 21, suggesting that this
population was expanding or that CD13NEG cells were lost from the
culture.
[0353] Based on these results, the sorting strategy shown in FIG.
12B was developed which omits the contaminating partially
reprogrammed CD13POSSSEA4POS population by selecting the highest
Tra-1-60POS expressing cells within the CD13NEGSSEA4POS population.
Using this strategy FACS was used to derive 228 individual iPSC
lines from over 75 fresh or frozen fibroblast lines generated from
biopsies harvested from healthy or disease patients using either
integrating (retroviral) or non-integrating (Sendai virus)
reprogramming vectors and extensive characterization was performed
on a subset of those lines which is described in the data that
follows. The first 2 weeks of the reprogramming process was further
characterized on 128 FACS derived iPSC lines using the analysis
structure shown in FIG. 11D. As shown in FIG. 12C, a higher
percentage of SSEA4POSTra-1-60POS cells were generated in Sendai
infections compared to retroviral infections over the entire time
course. However, Sendai infections demonstrated a delayed reduction
in the proportion of CD13POSSSEA4POSTra-1-60POS cells FIG. 12D. By
the second week of induction, the proportion of the CD13POS
population between the cultures was similar.
FACS Derived Lines are Pluripotent
[0354] To further characterize this defined selection strategy, the
phenotype and function of the FACS-derived iPSC clones were
compared to manually picked clones. First, the 0825, 1018, and 1023
fibroblast lines shown in FIG. 12A reprogrammed using the 4-factor
retroviral protocol were subjected to either FACS derivation at 7
dpi or standard picking techniques. For each method, one clone from
each line was randomly selected for expansion and further
characterization by a standard battery of assays, including
karyotypic analysis, DNA fingerprint, pluripotent surface marker
expression, qRT-PCR, and Embryoid body (EB) and teratoma formation.
All fibroblasts and reprogrammed iPSC lines displayed normal
karyotypes, and had DNA fingerprints matching the parental
fibroblast line (Table 4). Clones from the 0825 foreskin fibroblast
line had a DNA fingerprint that matched a major subpopulation in
the parental fibroblasts that contained a contaminating
subpopulation with a different genotype, suggesting isolation of
clonal cultures from a mixed population.
[0355] Both the manually and FACS-derived iPSC lines expressed
common markers of pluripotency, including the surface marker
Tra-1-60 and the transcription factor Nanog, and generated compact
colonies morphologically consistent with normal hESCs, FIG. 19
(A-B). Next, the cell lines were expanded for ten passages and the
expression of endogenous Nanog, Oct4, Sox2, cMyc, and Klf4, and
silencing of the viral transgenes Oct4, Sox2, Klf4, and cMyc were
assayed. A probe-based Nanostring nCounter transcript
quantification assay was used to assess pluripotency by detecting
both activation of endogenous gene expression FIG. 13A and
silencing of retroviral transgenes FIG. 13B. These data were
further confirmed by qPCR FIG. 19 and revealed a similar pattern of
endogenous gene expression in all iPSC lines compared to
undifferentiated hESC controls FIG. 13A, FIG. 19. However, two of
the three manually derived clones (1018.sub.--2 and 1023_C)
maintained much higher expression of the viral transgenes than the
sorted clones FIG. 3B. Additionally, the 1018.sub.--2 cultures
expressed CD13, indicating the presence of non-reprogrammed or
partially transformed human fibroblasts in the manually picked
lines FIG. 13B. These analyses suggest that selection of single
cells based on CD13NEGSSEA4POSTra-1-60POS expression can be used to
select against partially reprogrammed or contaminating cell types
in reprogrammed cultures. The full data set for these experiments
is provided in Table S7 (see Kahler et al, 2013, incorporated
herein by reference).
[0356] Modified pluripotent scorecard assay was performed on
manually and FACS derived clones to demonstrate (A) activation of
endogenous gene expression and (B) silencing of gene expression and
presence of unreprogrammed and transformed fibroblasts CD13POS in
manually derived clones. (C) Three sorted and three picked lines
from patient 1023 were used to compare the ability of both methods
to generate independent clones. 10.mu. of genomic DNA were cut
overnight with BglII and submitted to Southern blotting. The HUES
line HES2 was used as a positive control for endogenous KLF4/OCT4,
and as a negative control for transgene insertions. Samples were
first blotted for KLF4, then stripped and reblotted for OCT4.
Picked clones 1023 C and E are consistent with being the same clone
by both KLF4 and OCT4 blotting. * indicated the predicted
endogenous KLF4/OCT4 bands, and ** indicated a consistent band
found in all samples blotted with OCT4.
[0357] We next examined undirected EB formation to measure the in
vitro differentiation potential of FACS and manually-derived iPSCs
clones. Following differentiation for 5 weeks, EBs were collected
and assayed for markers of three embryonic germ layers endoderm,
mesoderm, and ectoderm by immunohistochemistry for
.alpha.1-fetoprotein (AFP), smooth muscle actin (.alpha.SMA), and
beta III tubulin (Tuj1), respectively. EBs derived from FACS or
manually picked clones expressed markers associated with formation
of the three germ layers FIG. 14A-B. To further define the
differentiation potential of the derived lines, RNA from the EBs
were collected after two weeks of differentiation and tested
against a panel of lineage-specific nCounter probes Table S4
previously validated to detect expression of genes commonly found
in the three germ layers [15] FIG. 14C. With the exception of the
FACS-derived 0825 line, all lines expressed comparable levels of
the germ layer-associated genes, indicating they have similar
potential to spontaneously differentiate in vitro into any germ
layer. The full data set for these experiments is provided in Table
S8 (see Kahler et al, 2013, incorporated herein by reference).
[0358] Embryoid bodies were derived from FACS (A) or manually
derived clones (B) and stained for expression of alpha fetoprotein,
smooth muscle actin and beta III tubulin (Tuj1) to demonstrate
differentiation potential in vitro potential. 10.times.
Magnification (C) Differentiation potential of the derived lines
for expression of germ layer genes present in the Lineage scorecard
assay. (D) Teratomas from FACS (D) or manually derived (E) clones
of 1023 fibroblast line indicating in vitro differentiation
potential by formation of three germ layers.
[0359] To measure the in vivo differentiation potential of the
iPSCs, immunocompromised mice were injected with FACS or manually
derived clones from the 1023 fibroblast line. The resulting
teratomas were sectioned and examined by H&E staining. This
analysis showed that teratomas generated from sorted FIG. 14D or
manually derived FIG. 14E clones formed all three germ layer
tissues, including gut-like epithelial tissues (endoderm),
cartilage (mesoderm), and retinal pigment epithelium (ectoderm).
Together, these analyses validate the use of
CD13NEGSSEA4POSTra-1-60POS expression as a surface marker signature
compatible with FACS that can be used to isolate a population of
fully reprogrammed iPSCs.
FACS Derivation Produces Independent Clones
[0360] Because iPSC lines can arise from rare apparently stochastic
events at early time points during reprogramming, it was important
to establish that FACS sorting could isolate multiple independent
reprogramming events. To determine whether FACS derivation can
produce unique cell lines in a similar manner to manual picking,
Southern blotting was performed on several clones derived by both
methods. Klf4 and Oct4 probes were used to identify the endogenous
and virally integrated forms of the genes. Different banding
patterns indicate differences in the chromosomal integration sites
and, in some cases, varying numbers of detectable integration
events. As shown in FIG. 13C, all three sorted clones from line
1023 have different integration sites for both Klf4 and Oct4,
demonstrating they are independent clones. In contrast, two of the
three picked clones from line 1023 have identical banding patterns
for Klf4 and Oct4, suggesting they are the same clone. Of the iPSC
lines generated from three different fibroblast lines, 8/9
FACS-derived lines were independent clones, while 7/9 manually
picked lines were independent (data not shown), suggesting
equivalent ability to generate clonal cultures. Therefore, FACS
sorting between 7-14 dpi using of CD13NEGSSEA4POSTra-1-60POS can
generate independent clonal cultures following retroviral
reprogramming.
FACS Derived Lines are Stable at Later Passages
[0361] To demonstrate the stability of FACS derived iPS clones at
later passages, a foreskin fibroblast line (0819) was retrovirally
reprogrammed using both FACS and manual derivation methods. Three
individual clones were chosen from each derivation method and
expanded on MEFs to asses pluripotent surface marker expression by
FCM at later passages. As shown in the first row of FIG. 15A-B,
cultures of all clones (C1-C6) resulting from each derivation
method possessed populations of cells positively expressing both
SSEA4 and Tra-1-60 at varying proportions indicating stability at
between 12-14 passages. Although not shown in FIG. 15, cultures of
these clones were stable at earlier (p4-p11) and later (p20-p25)
passages. Clones C3 and C6 were adapted to matrigel and mTser media
(*C3 and *C6 in FIG. 15A,B) following 11 passages on MEFS and
expanded for 3-5 passages to demonstrate the stability of FACS
derived iPS lines following changes in substrate and media
conditions. FCM analysis of Matrigel adapted iPS lines show stable
surface marker expression with less SSEA4POSTra-1-60NEG populations
than the manually derived clone C6. Small populations of CD13POS
expressing both Tra-1-60POS and Tra-1-60NEG (second row of FIG.
15A-B) were present in all cultures with the exception of the FACS
derived C3 and *C3 clones indicating the variability present in
individual clones derived under DNA integrating reprogramming
techniques. Similar results are observed within clones derived
using the non-integrating Sendai viral platform. These results
demonstrate that FACS derived iPS clones remain stable over
multiple passages and following adaptation to feeder free
conditions.
[0362] Three individual clones were selected from foreskin (0819)
fibroblasts lines which previously underwent four factor retroviral
reprogramming and were derived by either FACS (A, C1-C3) or manual
(B, C4-C6) techniques were analyzed by flow cytometry for
pluripotent surface marker expression following expansion on murine
embryonic fibroblasts for 12-14 passages. Clones C3 and C6 were
adapted to Matrigel and mTSER media around passage11 and expanded
for several passages prior to surface marker analysis by flow
cytometry to demonstrate stability following changes in culture
conditions. Events displayed in the 2D scatter plots are "live"
cells as defined by forward and side scatter properties expressing
indicated surface markers.
Utility for Multiple Reprogramming Methods
[0363] To further validate that the FACS surface marker panel can
be used for multiple reprogramming methods, fibroblasts were
reprogrammed using non-integrating Sendai viral constructs carrying
the four Yamanaka reprogramming factors and compared the FACS and
manual derivation methods to determine if there were differences
between the integrating and non-integrating reprogramming systems.
For these studies, an adult fibroblast line (131) was infected and
subjected to either FACS sorting at 11 dpi or to manual derivation.
At 11 dpi, the fraction of SSEA4POSTRA-1-60POS cells that were also
CD13POS was significantly lower (1-2%) than with retroviral
reprogramming (37-54%, FIG. 12C), suggesting an accelerated rate of
reprogramming. As before with the retroviral lines, several clones
from each derivation technique were selected and expanded for
characterization following confirmation that the parent fibroblast
line possessed a normal karyotype and DNA fingerprint, and was free
of contaminating cell lines FIG. 18.
[0364] As before, individual clones selected from both FACS and
manual derivation techniques expressed the common markers of
pluripotency, as revealed by immunostaining FIG. 16A-D. In
addition, the sorted (SRT) and picked (PCK) clones showed
comparable levels of endogenous Oct4, Sox2, KLF4, MYC, and Nanog
gene expression as early as passage 5, which remained relatively
constant to passage 10, FIG. 16E. Similarly, though greatly reduced
compared to control infected fibroblasts, Sendai virus gene
expression was slightly above background at passage 5 in one sorted
and one picked clone. However, this Sendai gene expression was
eliminated by passage 10 in both cases, FIG. 16F. The full data set
for these experiments is provided in Table S9 (see Kahler et al,
2013, incorporated herein by reference).
[0365] Immunofluroescence microscopy of the 1001.131.01 line
demonstrating expression of common markers of pluripotency by FACS
or Manually Derived IPSC lines. Nuclear Transcription Factors shown
in Green, Surface Markers shown in Red, Nucleus stained with DAPI
in Blue (A) Nanog/Tra-1-60 (B) Oct4/Tra-1-81 (C) Sox2/SSEA4 (D)
Oct4/Alkaline Phosphatase. 10.times. Magnification (E) Expression
of endogenous pluripotent transcription factors (F) Silencing of
viral transcription factors occur by passage 5. (G) Expression
levels of transcription factors common to the indicated germ layers
from EB generated by the indicated IPSC lines.
[0366] The in vitro differentiation potential of FACS and manually
derived iPSC clones reprogrammed by the Sendai virus protocol was
evaluated by EB formation and a lineage specific nCounter assay as
above. Similar trends in gene expression were observed for clones
derived under both methods, FIG. 16G. Both sorted and picked lines
expressed levels of the ectodermal marker FGFR2 comparable to that
of the control HUES42 line but higher levels of the mesodermal
marker HHEX. Most clones showed levels of endodermal gene
expression comparable to the HUES42 line with the exception of a
manually derived clone that expressed higher levels of GATA6 than
the remaining picked lines or FACS-derived lines. The full data set
for these experiments is provided in Table S10 (see Kahler et al,
2013, incorporated herein by reference). Collectively, these data
demonstrate that using FACS to purify the
CD13NEGSSEA4POSTra-1-60POS cells from either retroviral or Sendai
viral 4-factor reprogramming protocols consistently produces high
quality iPSC lines.
Discussion
[0367] Clinical application of iPSC technology will require
standardized and reproducible methods for each step of derivation
and differentiation into relevant cell types. The majority of
manually derived iPSC lines were found to contain CD13POS cells
even after prolonged culture suggesting that these lines were
either not fully reprogrammed or that CD13POS cells were carried
over during passage. While both manual picking and FACS sorting
methods [10] have been used to isolate reprogrammed pluripotent
cells, inclusion of a negative selection marker such as CD13 has
significant advantages in improving the purity of reprogrammed
cultures. This fact was previously demonstrated [13]. Here,
findings have validated a surface marker profile that enables
selection of early reprogrammed iPSCs following reprogramming with
either DNA-integrating or non-integrating viruses by FACS.
Employing this strategy as early as 7 dpi isolates a highly
purified starting population of fully functional
CD13NEGSSEA4POSTra-1-60POS cells that are depleted of contaminating
non-transduced and transformed fibroblasts. 228 individual iPSC
lines have been successfully generated and characterized in 2 years
from 76 fibroblast lines obtained from fresh biopsies, frozen
stocks, and cell line repositories harvested from healthy and
individuals possessing various forms of diabetes,
neurodegenerative, cardiac and autoimmune diseases. Table 8,
below.
TABLE-US-00008 TABLE 8 Summary of FACS Derived hIPSC Lines (S6)
Cell Total Model* Lines Derivations Retro Sendai Alzheimer 11 20 19
1 Parkinsons 4 8 2 6 FTD 2 2 0 2 GAN 5 14 14 0 Cardiac_LMNA 3 7 6 1
Cardiac_LongQT 6 14 14 0 MODY 11 34 24 10 T1D 3 24 17 7 T2D 1 8 8 0
MS_RR 1 2 0 2 MS_SP 1 1 0 1 Control 28 94 51 43 Totals 76 228 155
73 *MS_RR Multiple Sclerosis Relapsing Remitting, MS_SP Multiple
Sclerosis Secondary Progressive, FTD Frontal Temporal Dementia, GAN
Giant Axonal Neuropathy, LMNA Lamin A/C, MODY Mature Onset Diabetes
of the Young
[0368] Moreover, FACS is routinely used for maintenance of
established cell lines to remove differentiated cells and to
dispense graded numbers of highly purified
CD13NEGSSEA4POSTra-1-60POS populations cells for use in
high-throughput derivation and screening assays which include
directed differentiation and automated drug screening and
phenotyping experiments. This is an important property because the
results of these assays could be unequivocally attributed to a
defined population of reprogrammed cells rather than to a
heterogeneous mixture of cells. Taken together, these results
suggest that isolation of the CD13NEGSSEA4POSTra-1-60POS population
following reprogramming, including integrating or non-integrating
viral technologies, allows for the rapid isolation of high quality
iPSC lines. Negative selection against CD13POS cells significantly
reduces the appearance of transformed cells in ipsc cultures and
suggests that negative selection for a marker present on the
starting somatic cells can be used to exclude non-reprogrammed or
transformed cells from the cultures. Future studies will be needed
to determine if this strategy applies to derivation from other
somatic cell types or reprogramming methods.
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(2009) A chemical platform for improved induction of human iPSCs.
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Example 4
Generation of Large Genetically Diverse Cell Panels
[0388] A tissue procurement process has been established through
which over 500 genetically diverse skin samples have been collected
representing approximately 79% of the ethnic diversity needed to
model the U.S. population (based on U.S. census data). 500
fibroblast lines have been generated from these samples and 300
iPSC lines using an automated system as described herein, with work
continuing to generate more lines and to expand the sample set
further. The cell lines produced are provided in 96-well microtiter
plates with each well containing cells derived from a different
individual.
[0389] Somatic cells are isolated, expanded, and analyzed for copy
number variations (CNVs) to determine karyotype and a genomic
identifier. High-content imaging is used to collect data cellular
growth rates, cell counts, and morphology that guide reprogramming
and differentiation. Non-genomic integrating reprogramming is
accomplished using transduction of five individual mRNAs expressing
Oct4, Sox2, Klf4, Lin28, and cMyc (see, for example, Warren et al.,
2010). The process is performed in a chemically-defined, xeno-free,
media to minimize potential sources of variability in resulting
cell populations. Clonal selection is achieved using a multi-stage
process including a magnetic bead based enrichment scheme where
non-reprogrammed cells are depleted from the cultures of iPSCs by
negative selection of CD13 and high-content imaging of surface
marker Tra-1-60. The resulting iPSCs are transferred to a 96-well
plate where colony growth is monitored using the automated
high-content imager. For further characterization of the iPSCs,
transcriptional analysis is performed by direct mRNA measurements
of a set of 100 gene probes covering pluripotency, all three germ
layers, sex, and housekeeping pathways. This analysis is performed
on the iPSCs as well as embryoid bodies (EBs) generated from
them.
Example 5
A Fully Automated, High Throughput Platform for iPS Cell Derivation
and Characterization
[0390] Induced pluripotent stem cells (iPSCs) have become an
essential tool for modeling how causal genetic variants impact
cellular function in disease and are an emerging source of tissue
for transplantation medicine. Unfortunately, the preparation of
somatic cells, their reprogramming and the subsequent verification
of iPSC pluripotency are laborious, manual processes that limit the
scale and level of reproducibility of this technology. The present
Example describes a robotic platform for iPSC reprogramming that
enables high-throughput conversion of skin biopsies into iPSC lines
with minimal human intervention. Importantly, iPSC lines
manufactured by this automated system exhibited significantly less
variation than those produced manually. This robotic platform thus
enables the application of iPSCs to population-scale biomedical
problems including the study of complex genetic disease and the
development of personalized medicines.
Introduction
[0391] The reprogramming of somatic cells into induced pluripotent
stem cells (iPSCs), coupled with the development of methods for
directing stem cell differentiation into relevant cell types,
offers an unprecedented opportunity to study the cellular
phenotypes that underlie disease (Takahashi and Yamanaka, 2006;
Takahashi et al., 2007; Rubin, 2008; Colman and Dreesen, 2009;
Nishikawa, Goldstein and Nierras, 2008; Daley, 2010). Study of
these emerging "stem cell disease models" has led to new
mechanistic insights into a wide variety of conditions ranging from
neurological disorders to cardiovascular and infectious disease
(Robinton and Daley, 2012).
[0392] One limitation of the application of these methods is the
substantial level of variation between different stem cell lines
that arises during the reprogramming progress, affecting both
functional properties of the lines and their performance in
disease-related studies. As a result, most successful reports have
relied on evaluation of several cell lines derived from individuals
harboring genetic variants of high penetrance. If stem cell
technologies are to be applied to the study of common genetic
variants that confer only modest effects but have been shown to be
important contributors to conditions such as schizophrenia, and
metabolic disease (Morris et al., 2012; Ripke et al., 2013), it
will be essential to minimize variation arising during
reprogramming, subsequent stem cell expansion and differentiation.
Reduction in this source of variation would increase resolution of
the phenotypic effects contributed by the genotype of a particular
individual.
[0393] Presently, it remains unclear what fraction of or the extent
to which variation between iPS cell lines arises from technical
aspects of the procedure, rather than from uncontrollable,
stochastic epigenetic events that occur during reprogramming.
Possible contributors to functional variation include genetic
background and tissue source, {reviewed in (Cahan and Daley, 2013;
Nestor and Noggle, 2013); reprogramming factor stoichiometry during
delivery (Carey et al., 2011); and stress during culture (Liang and
Zhang, 2013). Additionally, a growing number of methods are used to
deliver reprogramming factors and various cell culture media and
substrates have been used for downstream expansion (Chen et al.,
2014), This lack of standardization likely introduces additional
variability among cell lines established by different laboratories
(Newman and Cooper, 2010). As automation has improved precision and
scalability in many areas of biomedical research (Meldrum, 2000;
Meldrum, 2000; Lander et al., 2001), developing a fully automated
platform for iPS cell derivation, expansion and differentiation
would allow identification of and restriction of the factors
contributing to variability in stem cell line behavior.
[0394] The present Example describes the development of three
integrated robotic systems that automate the entire process of
deriving iPSC lines. This integrated reprogramming platform was
used to systematically explore several variables that have been
reported to be important sources of variation in the reprogramming
process. Importantly, automation alone was found to eliminate a
significant portion of the variation in differentiation propensity
exhibited between iPS cell lines.
Results
Automated Fibroblast Production
[0395] As a first step in developing an integrated and automated
process for deriving iPSCs (FIG. 20A), a robotic system has been
established for isolating skin fibroblasts from volunteer biopsies
and tissue samples (FIG. 20A, Stage 1). This system processes
tissue under quarantine conditions prior to mycoplasma testing,
allowing for the expansion and freezing of fibroblasts before being
transferred into a cleaner culture environment. The system is
housed in a BSL II biosafety hood (FIG. 20B) and integrates a
robotic liquid handler with an automated centrifuge, microscope and
incubator. The biopsy processing system is complemented by a
second, independent liquid handling robot connected to a
luminescence plate reader, used to conduct mycoplasma detection
assays.
[0396] For fibroblast derivation, biopsies and tissue samples were
manually dissected and placed into individual plates filled with a
low serum culture media selected to eliminate batch to batch
variation in serum. In addition, low serum medium is more
compatible with down-stream reprogramming using modified RNAs
(Warren et al., 2010). All further maintenance, including passaging
and feeding, was performed via automation. Every five days biopsy
outgrowth was measured through automated image acquisition and
quantification (FIGS. 20C and D). Media exchanges and media
collection for mycoplasma testing were also handled in an automated
fashion. Multi-well plates of media collected for mycoplasma
testing were then placed onto the second platform for automated
testing (FIG. 27A). Following completion of mycoplasma testing,
fibroblast outgrowths were enzymatically passaged by the system
into new plates for further expansion.
[0397] After one passage, in order to minimize population doublings
and increase reprogramming potential (Utikal et al., 2009),
fibroblasts were frozen into multiple 2D barcoded cryovials and
banked to produce low passage frozen stocks. The automated imaging
system first identified wells with outgrowth (FIG. 20Di) and area
of the culture plate occupied to calculate a confluence value (FIG.
20Dii). In some experiments, DNA staining and algorithms were used
for identifying and counting nuclei to extrapolate cell counts from
confluence values using standard curves (FIG. 20Diii and 20Div).
This allowed non-invasive calculation of growth rates of the
fibroblasts. As early experiments suggested that fewer than 100,000
cells were needed for reprogramming, yields of fibroblasts from
outgrowths at this early stage of growth were sufficient for the
subsequent reprogramming steps (778,216 cells per passaged well of
a 6-well dish s.d.=88,813, n=60). This allowed the cells to be
frozen at the second passage. One vial was typically reserved for
iPS generation through short-term storage within an automated
-80.degree. C. sample access manager, with the remainder banked in
liquid nitrogen. An average of 363,000 fibroblasts were produced
per sample (s.d. of 305,000, n=168) with minimal expansion
(passaging of the biopsy outgrowth results in p1 cultures). The
average total number of cells frozen into a single cryotube at the
time of freezing was 121,437 cells which upon thawing had an
average viability of 84%.+-.1.43% (mean.+-.SEM, n=167).
[0398] During development of the automated system, a total of 640
skin tissue samples were processed with 89.4% producing fibroblasts
that were successfully frozen (n=572). Failures that arose were
primarily due to either bacterial or fungal contamination (4.7%,
n=30) attributable to sample handling before entering the system,
and were minimally associated with equipment or manual process
failures (3.2%, n=21). Only 2.7% (n=17) did not show outgrowth,
which could be attributed to the small size of the biopsy, lacking
an overt dermal layer. Using a Nanostring nCounter karyotyping
assay that can detect aneuploidy as well as large chromosomal
gains/losses (FIG. 27B), 20 randomly selected, representative
fibroblast samples were tested. The majority of samples (19/20,
95%) showed a normal diploid karyotype (46XX or 46XY). Thus, the
automated process can successfully derive, expand and cryopreserve
high quality, low passage fibroblasts which can be banked for
further processing or future use.
[0399] To monitor fibroblast growth rates and cell culture
densities of the resulting plates, the automated imaging system was
used (FIG. 20Dii). Various approaches were tested for monitoring
fibroblast growth and found that confluence measurements (percent
of well covered by cells) were sufficient to allow reliable
tracking of growth rates. Frequent measurements allowed for
doubling time calculations to be performed during log phase growth.
Under these low-serum conditions, average fibroblast doubling time
was 66 hours (s.d.=30.2 h, n=298). (FIG. 20E). This modest doubling
time is not believed to be a product of growth on the automated
system per se as when a subset of these samples was robotically fed
with serum-containing media the doubling time was decreased to 45.8
hr (s.d.=16.5 h, n=33). While the mean doubling rates did not
significantly differ from their growth rates prior to freezing
(p=0.69), the variation decreased by almost half upon recovery in
serum (% CV=61% before vs. 36% after thaw) (FIG. 20G). As doubling
rate did not correlate with age (FIG. 20F), this suggests it should
be possible to group samples with similar growth characteristics
soon after initial outgrowth to establish cultures for downstream
automated reprogramming as described below.
Automated iPS Reprogramming
[0400] To enable automated reprogramming, an integrated robotic
platform was constructed with the capacity to thaw fibroblast
samples, deliver reprogramming factors via Sendai virus
transduction (Fusaki et al., 2009) or modified mRNA transfection
(Warren et al., 2010), perform magnetic selection of reprogrammed
cells, and finally image cultures to identify nacent stem cell
colonies after surface marker staining (FIG. 20A, Stage 2, and FIG.
21A).
[0401] First, a viral infection method using Sendai virus (Fusaki
et al., 2009) was adapted to the automated liquid handling system.
Automated delivery of Sendai virus to 50,000 fibroblasts at a
moiety of infection of 4 resulted in 2 to 10 TRA-1-60 positive
colonies per well under feeder free conditions. Similar
efficiencies were obtained by manual delivery under these
conditions. Several lines were derived by manual picking of
TRA-1-60 positive colonies after automated infection and appearance
of colonies (FIG. 28B) before continuing the culture of the picked
colonies on the automated system. Established cultures from these
colonies expressed common markers of pluripotency, including Nanog,
Oct4, SSEA4 and TRA-1-60 (FIG. 28C). Consistent with previous
results (Kahler et al., 2013), automated Sendai infections induce
TRA-1-60 positive cells that retain surface expression of a
fibroblast marker with an average of 58.2% (n=12) of
TRA-1-60+/SSEA4+ were also CD13+(FIG. 28D). Further, after
differentiation in EB assays (see below), significant clonal
variability was found in gene expression that appeared to coincide
with residual Sendai transgene expression remaining in the lines
between passages 5 and 10 (FIG. 28E). Between passages 11 and 12,
the Sendai lines were incubated at 38.5.degree. C. to encourage
Sendai inactivation (specifically C-Myc) at which point a decrease
in Sendai virus expression was observed. However, after a further
2-3 passages, the lines were reanalyzed and Sendai transgene
expression had again increased. Additionally, variability in
toxicity was noted among different lots and batches of virus.
Together, these results suggested that, while it is possible to use
Sendai virus to reprogram fibroblasts by automated methods, it was
unlikely to emerge as a preferred method.
[0402] Next, transfection methods were adapted to deliver modified
mRNA (Warren et al., 2010) to reprogram fibroblasts by automation.
After automated passaging, fibroblasts were treated via automated
media exchange with B18R to block interferon response. The liquid
handling system was also used to deliver transfection mix
containing miRNA (Miyoshi et al., 2011) followed by 10 daily
transfections of base modified mRNA encoding Oct4, Klf4, Sox2,
c-Myc, Lin-28, and nuclear GFP (nGFP) (FIG. 21B). The miRNA was
also included together with the fourth mRNA transfection. Human
fibroblast conditioned media was replaced daily by automated media
exchanges before each transfection. Six days after final
transfection the cultures were transitioned to a feeder-free hES
cell culture medium using automated partial media exchanges. This
integrated automated process was tested by performing 20
consecutive experimental reprogramming runs of 24 fibroblast
samples in duplicate and under varying conditions, for a total of
960 independent reprogramming experiments (FIG. 21A).
[0403] In addition to adult donor fibroblasts, BJ foreskin
fibroblasts were included in each run to control for run to run
variability. Following this protocol, nascent iPSC colonies were
consistently observed between 16 and 22 days of culture (FIG. 21C,
D). Established cultures demonstrated pluripotent hESC-like
morphology and expressed common markers of pluripotency, including
Nanog, Oct4, Sox2, SSEA4 and TRA-1-81 (FIG. 28A). Over all runs, an
average of 7 TRA-1-60+ colonies were induced per well (n=299, range
1-40 colonies). These cultures contained a high proportion of
TRA-1-60+/SSEA4+ cells and an average of 9.7% (n=38) of cells
retained CD13 (FIG. 21E). Reprogramming efficiency was between
0.001% and 0.16% for successful attempts per plated somatic cell,
consistent with previous results obtained under feeder free
conditions (Warren et al., 2012), and was slightly higher for
control BJ fibroblasts (0.43%) than for adult fibroblast cultures
(0.014%).
[0404] The next analysis investigated the factors that correlated
with reprogramming success rates. The number of colonies produced
per well was determined after mRNA mediated reprogramming
production runs and several parameters were compared during
fibroblast recovery and reprogramming. The number of colonies was
determined by automated image based colony identification and
counting after TRA-1-60 live cell surface staining of the cultures
(FIG. 21D). Although fibroblasts from older donors were
successfully reprogrammed, increasing donor age negatively
influenced the number of colonies produced. Additionally, slower
proliferation rates during reprogramming as well as the presence of
serum during fibroblast recovery and passaging all had a negative
impact on the number of colonies produced, when controlling for
other variables included in the analysis (FIG. 21F-I). This is
consistent with a transition from serum containing media to
serum-free media reducing proliferation rates important for
reprogramming success. Together, these results define conditions
that allow for the derivation of iPSCs using this automated
process.
Automated iPS Purification
[0405] FACS methods have previously been described for enriching
reprogrammed iPSCs using a standard panel of cell surface markers
(Example 3 above, and Kahler et al., 2013). In particular,
incompletely reprogrammed cells often retain surface expression of
fibroblast specific markers. To achieve a greater throughput,
reprogrammed iPS cells were enriched using automated magnetic bead
based negative selection to remove incompletely reprogrammed cells
(FIG. 22A). Through the integration of a MultiMACS multi-well
magnetic bead separation device into the liquid handling system,
negative selection was used to, in parallel process 24 lines at a
time (FIG. 22B). To test the system, spike in experiments were
performed with an iPS cell-to-fibroblast ratio of between 1:20 and
1:100 that demonstrated that a 6-fold fibroblast depletion and an
average 47-fold iPS cell enrichment could be achieved (FIG. 29A).
In practice, the magnetic bead selection process resulted in an
average of .about.30% CD13-/SSEA4+/TRA-1-60+ cells following
completion of the automated mRNA reprogramming protocol (FIG.
29B).
[0406] The population flow-through fraction of iPS cells by MACS
was then plated into 96-well plates. The flow-through fraction was
plated on an extracellular matrix in serum and feeder free
conditions in a three point, two-fold serial dilution in 12 wells
per initial reprogrammed well to recover colonies (FIG. 22D).
Starting as single cells at the first day after sorting,
TRA-1-60+colonies formed within 7-10 days (FIG. 22C) and had a
typical ES cell morphology (cells with large nuclei, small amount
of cytoplasm, with compact monolayer colony morphology). Doubling
times, calculated from daily confluence measurements using the
automated imaging system, ranged from 24-48 hrs for most lines.
Sorted cells were checked daily using the Celigo automated
microscope. Doubling times for most lines ranged from 24-48 hrs
(FIG. 22G). Additionally, it was retrospectively established that
clonal iPSC lines arose from expansion of single cells plated in
single wells (FIGS. 22E and 29C). After wells with uniform
confluence values were identified, three candidate wells per sample
were selected and consolidated 1 well to 1 well onto 96-well plates
by the robotic liquid handling methods for expansion and further
quality control assays. After this passaging step, flow cytometry
analysis further demonstrated that .about.80% of the cells were
SSEA4+/TRA-1-60+(FIG. 22F). These passaged iPSCs reestablished
typical human ES cell like colony morphology and expressed the
pluripotent marker NANOG (FIG. 30B). To further ensure the negative
selection had eliminated non-reprogrammed or partially reprogrammed
cells, the sorted cultures were further screened by gene expression
assays using a panel of pluripotency (NANOG, POU5F1, LIN28, ZFP42,
SOX2) and differentiation (ANPEP, NR2F2, AFP, SOX17) marker genes.
Using an analysis strategy similar to one previously described
(Bock et al., 2011), performance of candidate iPSC lines were
compared to an established reference panel of hESC lines (FIG. 23A,
B). A set of newly reprogrammed and sorted iPSC lines were tested
using this assay and 9 of 11 tested lines had scores consistent
with the hESC reference panel. Two of the lines tested showed
pluripotency scores consistent with reference standards, but showed
elevated differentiation scores (FIG. 30A). This could be
attributed to overgrowth of iPSCs resulting in spontaneous
differentiation in these cultures (FIG. 30C). Together, these data
suggest that iPSC lines purified by automated processes
demonstrated characteristics of reprogrammed pluripotent cells
within two passages after reprogramming. Thus, candidate iPSC lines
in 96-well format can be recovered by automated single well
passaging methods to consolidate and array multiple iPSC lines in
parallel for expansion and further analysis.
Automated Culture of Multiple iPSC Lines in Parallel
[0407] The primary aim for developing the automated process was to
allow parallel derivation and culture of multiple iPS cell lines in
parallel. The knowledge of growth rates and cell density at the
time of consolidation combined with the ability to bin and batch
cell lines and/or adjust plating characteristics at various steps
was hypothesized to further enable parallel culture of cell lines
with diverse growth characteristics at early passages (FIG. 22G).
To enable this, automated and informatic processes were developed
for cryopreservation of nascent iPSCs with similar growth
characteristics (FIG. 20A Stage 3, and FIGS. 24A and 31A). After
freezing in cryotubes followed by subsequent thaw, iPSCs recovered
to show a normal morphology (FIG. 24B). Correlations between
pre-freeze and post-thaw recovery confluencies were highest one day
after the thaw (Pearson's r>0.91) and they decreased as the
wells approached full confluence (Pearson's r>0.71 on day 3,
>0.41 on day 6), due to overgrowth of higher confluence wells
(FIG. 24C). The percentage of SSEA-4/Tra-1-60 double positive iPSCs
remained consistent before and after the thaw (FIG. 24E), with
subsequent passaging showing no significant differences in the
percentages of the SSEA-4+/Tra-1-60+ double positive population
(FIGS. 24D and 31D). Enzymatically robotically passaged cultures
formed morphologically ideal colonies with well defined edges and
expressed pluripotency markers POU5F1, Oct-4, Sox2, Nanog, SSEA-4,
Tra1-60 and Tra 1-81 (FIG. 31C). The cultures growing in 96-well
plates could be successfully maintained over 5-7 days growth and
before requiring passaging (FIG. 24F). Following expansion of a
single 96-well plate into three plates, between-plate variation
remained low (FIG. 31B). Additionally, the wells did not lose
SSEA-4+/Tra1-60+ pluripotency marker expression (FIG. 31D).
Passaging rations between 1:1 and 1:15 have been successfully
performed on the automated system. Together, these data indicate
that after freezing, the grouping and thawing of newly derived iPSC
lines, samples can successfully occur based on prior growth
characteristics. Subsequent expansion of these lines does not alter
either the growth or pluripotency characteristics allowing the
automation of parallel culture in a multiwall format.
[0408] Analysis of genomic DNA was performed to track cell line
identity (FIG. 31F-H) and to ensure that cell lines remained
karyotypically normal (FIG. 31E). iPS lines were karyotyped using
the Nanostring nCounter karyotyping assay that can detect
aneuploidy as well as large chromosomal gains/losses commonly found
during manual pluripotent stem cell culture. Whilst previous
reports have stated that chromosomal abnormalities arise in
approximately 20% of iPSCs (Mayshar et al., 2010), the majority of
the presently described iPSCs (89%, n=38) showed a normal diploid
karyotype (46, XX or 46, XY). Of the 4 abnormal lines detected, one
had a chromosomal gain in the long arm of chromosome 22 (probes
spanned 22q11.21-22q13.32). The remaining 3 abnormal lines all
shared a common starting fibroblast population and shared a copy
number gain in chromosome 17 (probes spanned 17q21.32-17q25.3),
suggesting heterogeneity of the original fibroblast population that
was below the threshold of detection. Together, these results
suggest that it is possible to maintain iPSCs during subsequent
automated passaging.
Automated Analysis of Differentiation Propensity
[0409] To assess the differentiation potential of robotically
derived iPSCs, a robotic platform was developed to generate EBs and
the ability of iPSCs to spontaneously differentiate into the three
germ layers was measured. Several automation compatible methods for
reproducibly forming EBs were tested followed by an automated
process to harvest and lyse EBs before using a Nanostring gene
expression assay to quantitatively assess germ layer
differentiation as previously described (Bock et al, 2011). The
previous assay was modified to include the 83 germ layer lineage
genes divided into ectoderm (EC), mesoderm (ME), and endoderm (EN)
gene sets as well as probes for transgene silencing and Sendai
vector elimination, sex (SRY and XIST), pluripotency (Oct4, POU5F1,
Sox2, Nanog, ZFP42), and housekeeping gene expression (ACTB,
POLR2A, ALAS1). In initial pilot studies, hierarchical clustering
of EB gene expression suggested that that samples group together
according to the type of method used for the EB formation assay.
EBs formed by hanging drop methods clustered separately from those
produced by plating in V-bottom plates. Expression of these gene
sets was measured relative to those from a control panel of EBs
made from hESC lines analyzed in parallel under identical culture
conditions (FIG. 32A-B). Pluripotency of the hESC lines used for
reference standards was verified by marker staining for POU5F1,
Oct4, TRA-1-80, Nanog, SSEA4, SOX2, TRA-1-60, and Alkaline
Phosphatase (FIG. 32A). All lines tested exhibited scorecard
differentiation propensities consistent with the ability to
differentiate into the three germ layers (FIG. 32B). Germ layer
lineage marker gene sets were differentially expressed between the
different methods of forming EBs (FIG. 25A), with hanging drop
methods generating gene expression biased towards endoderm and
V-bottom plates demonstrated a more uniform differentiation
potential. Together, this suggests that different methods of
generating EBs may confound comparisons among lines and highlights
the need for method standardization.
[0410] EB formation was optimized using EGFP marked iPSC lines, to
seed cells from a single well of a 96-well plate into six wells of
96 well V-bottom plates (FIG. 25B-C). Before EBs were collected,
plates were imaged using Celigo to monitor EBs formation (FIG.
25B). These automated methods allowed the iPSCs to aggregate and
form embryoid bodies at the bottom of the well (FIG. 25C). While
the differentiation propensity scorecard values for all samples
showed excellent correlation with those previously published (Bock
et al., 2011), a slight decrease was noted in correlation with
previously published data from identical reference lines grown
under different culture conditions (FIG. 25D-F), suggesting that
the assay is sensitive to differentiation culture conditions.
Therefore comparisons were made using reference data generated from
hESCs adapted to the culture conditions used to derive iPSCs on the
automated system.
Reduced Variation in Robotically Derived iPSCs
[0411] Next, the propensity of robotically derived iPSCs to
differentiate by the automated EB assay was measured and lineage
scorecard analysis was carried out described above was used (Bock
et al., 2011). Hierarchical clustering of gene expression shows
overall consistency of the IPSCs generated by automation. However,
the lineage scorecard differentiation assay suggested that it might
be possible to distinguish among variations in methods used to
derive the iPSC lines independent of genotype. It was found that
iPSCs derived through complete automation of the reprogramming
process showed reduced variation (as measured by comparing
distributions of standard deviation of gene expression) when
compared to lines reprogrammed by manual processes (p
value=7.08.times.10-12, Wilcoxen signed rank test) (FIG. 26). This
was true in comparisons within a single genotype (BJs, p
values=7.85.times.10-9) and as well as for the patient lines
(donor, p values=9.28.times.10-11) Interestingly, iPSCs initially
reprogrammed robotically before having colonies manually picked and
then returned to the automated system for expansion showed elevated
expression similar to that found in existing manually derived iPSC
lines (p value=0.023. Thus this finding suggests that manual clone
selection may be an important source of variation. Additionally,
lines derived by Sendai infection and manual colony picking showed
similar variation to lines initially reprogrammed using automation
but completed through manual colony picking (p value=0.40). This
suggests that lines produced by the completely automated process
show reduced variation at early time-points after derivation
compared to lines derived by current manual procedures.
Discussion
[0412] This Example describes an embodiment of a fully automated
platform for reprogramming easily obtainable skin cells into iPSCs.
The described platform achieves reproducibility and population
scale iPSC derivation and differentiation, using an automated
approach based on recent advances in reprogramming and
characterization methods (Bock et al., 2011; Kahler et al, 2013;
Warren et al, 2010). A fully-robotic process has been established
for the generation of fibroblast banks, iPSC reprogramming, as well
as automated assays for assessing differentiation potential. The
creation of this platform allowed assessment of the sources of
functional variability between iPS cells. Importantly, sue to the
use of robotics, this has been achieved with both the precision and
scale that could previously not have been considered.
[0413] Most notably, manual selection of newly reprogrammed iPS
cell colonies was in itself found to be a substantial contributor
to cell line to cell line variation. Through automation of the
reprogramming process, more than a third of the variability that
existed between manually selected lines was eliminated. This
finding demonstrates that at very least, a substantial portion of
this variation had purely technical origins.
[0414] The large scale of the described experiments also allowed
investigation of the previously raised question of whether the
origin of the somatic cells and and/or their genetic background,
influenced stem cell line behavior. The production of many cell
lines from both a single somatic population (BJ fibroblasts) and
from multiple distinct individuals allowed investigation of this
issue. The results presented in this Example clearly show that the
level of variability between cell lines made from many donors was
not different from that found with lines from a single donor.
Previous studies suggest that genetic factors could be a
contributing factor to functional variance between iPS cell lines
(Kajiwara et al., 2012). However, this data suggests that if these
factors do contribute, the do so modestly in comparison to the
technical variation that can be resolved through automation.
[0415] Although it has been cited as a potential inhibitor of
reprogramming in the past, advancing age of the subject being
reprogrammed was not a significant modifier of reprogramming
efficiency. Instead, both the growth rate and confluence of cell
cultures at the time of reprogramming were found to be the primary
drivers of whether the automated approach succeeded in producing
iPS cells in each individual case. This finding seems consistent
with the observation that genetic factors which slow proliferation
of cells inhibit reprogramming (Hanna et al, 2009).
[0416] In addition to this, the reprogramming method used for
producing iPSCs had a substantial effect on cell line properties.
Although aspects of iPSC production using both mRNA delivery and
Sendai virus infection could be automated, incomplete eviction of
Sendai virus led to a substantial change in the signature of gene
expression in pluripotent cells. For this reason, plus previously
discussed issues with lot to lot variation and availability, a
modified mRNA reprogramming method as a standard protocol. However,
the flexibility of the system allows for the future adoption of
other reprogramming methods as these become available.
[0417] As described here, the integrated system has a capacity to
produce approximately 384 iPSC lines per month. Running a second
personnel shift using the current system could allow capacity to
double, resulting in the ability to produce 768 iPSC lines per
month. The advantage to this approach of automating production over
a manual process, however, is that capacity can be scaled with
additional systems with only a minimal increase in personnel time.
The timeline for producing seed stocks of characterized iPSC lines
from fibroblasts is approximately 12 weeks. Although the current
automated system may not yet be ideal for clinical grade iPSC,
evidence that the process can be automated suggests that a similar
system tailored to the clinical grade production is now feasible.
Together this increased scale and accelerated timeline should
enable many large-scale projects utilizing iPSCs (McKernan and
Watt, 2013).
[0418] In the future, the increased throughput of reprogramming and
reduced variability between the resulting lines should open a
number of new avenues for investigation. First, this approach
should allow investigation of cellular phenotypes for disease
states found in conditions that are caused by diverse mutations. At
the moment, most studies utilizing iPSCs for disease modeling have
focused on a small number of lines originating from individuals
harboring either a single or small number of highly penetrant
mutations. The expanded scale and reduced variation of the
automated system should lead to greatly improved statistical power
in addressing the question of whether a modest effect observed in
culture is a direct result of the genetic background of the subject
in question.
[0419] This increased sensitivity should assist in accurately
assessing the impact of common variants that influence human
health. Although these variants may only contribute modestly to the
overall phenotype in a given individual, their prevalence in
populations highlights their importance in understanding their role
in disease. The ability to accurately study such variants would
represent an important next phase for in vitro disease models. If
there is one common process that eventually leads to cellular
dysfunction in each particular disease, it may be possible to
devise a single strategy for inhibiting it, providing a therapeutic
for all patients. In contrast, it may be that subsets of patients
follow distinct paths towards disease. If this is the case, it will
be necessary to identify these distinct groups of patients so that
a therapeutic strategy that is specific to the particular path
their disease follows can be devised and appropriately
administered. As the system described here is designed to perform
standard cell culture manipulations, adaptation of this robotic
technology to directed differentiation should further enable the
discovery of molecular and genetic pathways that underlie our
traits and disease.
Experimental Procedures
Cell Lines
[0420] Recruitment of volunteers and biopsy collection and written
informed consent procedures were approved by Western Institutional
Review Board. Human embryonic stem cell lines were obtained from
the Harvard Stem Cell Institute. Additional reference iPSC lines
BC-1, ND1.4 and 2.0 were obtained from NIH Center for Regenerative
Medicine (Chen et al, 2011; Cheng et al., 2012).
Automated Systems Description
[0421] To accomplish fibroblast banking, iPSC generation, and iPSC
characterization and freezing, three integrated robotic platforms
were assembled from a combination of eight automated liquid
handlers (Hamilton STAR and STARlet), five incubators (Thermo
Cytomat), two robotic arms (Hamilton RackRunner), four automated
Celigo plate imaging systems (Nexcelom Bioscience), three cryotube
decappers (Hamilton), three plate centrifuges (Agilent Vspin), and
one plate sealer (Agilent PlateLoc). User initiated software method
scripts that communicate with the relevant instrumentation were
written using custom software on the Venus platform (Hamilton) to
automate individual process steps described below. Usage of shared
automated devices was controlled by a custom software reservation
system. Disposable conductive pipetting tips (Hamilton) were used
throughout processes and tip reuse was minimized during all process
steps to prevent cross contamination of cultures. Standard plate
formats and tubes were used and tracked by barcode. Liquid handling
procedures are tracked and logged providing process
traceability.
Automated Biopsy Outgrowth and Fibroblast Cell Culture
[0422] Dermal fibroblasts were derived from donor tissue samples
collected in biopsy collection medium (see extended methods below
for all media formulations). Samples were washed in Biopsy Plating
Media, cut into 1-2 mm pieces, added to a 6 well plate and dried
for 15 minutes after which, biopsy plating medium was added to
wells dropwise. Plates were left undisturbed for 10 days to allow
for initial outgrowth before being transferred to the robotic
system for automated culture and expansion, growth rate analysis,
mycoplasma testing and freezing.
Automated Reprogramming
[0423] Automated methods were used to thaw and seed fibroblasts
onto 12 well plates (Corning, #3513) then perform medium exchanges
every third day until reaching 70-90% confluence. Cells were
robotically dissociated using TrypLE Select CTS (Life Technologies,
#A12859-01), counted by automated imaging procedure after viability
staining using Hoechst (Sigma, #B2261) and Propidium Iodide (Life
Technologies, #P3566) followed by cell number calculation for
robotic transfer into a Geltrex.TM. (Life Technologies, #A14133)
coated 24 well plate (Corning, #3526). Reprogramming of fibroblasts
was performed using automated transfection and feeding methods to
deliver modified mRNA (Stemgent, #00-0071) and conditioned Pluriton
reprogramming medium supplemented with B18R (200 ng/mL) as per
manufacturer's instructions. After 15-20 days following the
initiation of reprogramming, cultures were transitioned to Freedom
media (Life Technologies, #A14577SA) for an additional 5-10 days,
after which cells were live stained with TRA-1-60 (Life
Technologies, #A13828) to identify iPS colonies by the automated
imaging system. Sendai virus infections were performed using an
automated infection protocol with virus preparations kept cold on a
chiller block located within the robotic platform.
Automated iPSC Purification
[0424] After reprogramming, iPS cells were enriched by automated
depletion of non-reprogrammed fibroblasts using a MultiMACS.TM.
system (Miltenyi Biotec, #130-050-601) integrated into a Hamilton
STAR liquid handling system using anti-human fibroblast microbeads
(Miltenyi Biotec, #130-050-601). The iPSCs were collected, seeded
into 4 wells of a 96-well imaging plate (BD Biosciences, #353219),
and serially diluted 3-fold in adjacent wells. Based upon growth
rates calculated from automated imaging, well confluency levels and
the presence of live TRA-1-60 surface marker expression, samples
were selected and robotically cherry-picked after bulk dissociation
with 0.05 mM EDTA (Life Technologies, #15575-020), and consolidated
into a new Geltrex-coated 96-well plate (Corning, #3599).
Automated iPSC Passaging
[0425] Automated methods were used to perform daily feeding and
imaging of consolidated iPS cell lines using Freedom medium. Upon
reaching 70-90% confluence, the cell were passaged using Accutase
(Life Technologies, #A11105-01). Growth medium was supplemented
with Thiazovivin (1 .mu.M; Stemgent, #04-0017) for the first 24 hrs
after passaging to promote cell survival, after which cells were
fed daily with growth medium.
Automated EB Formation
[0426] Cells were dissociated and plated for gravity aggregation
using the automated liquid handling systems in 96 well V-bottom
plates (Greiner, #651161) in the presence of human ES culture
medium without bFGF (see extended methods for formulation)
supplemented with 1 .mu.M Thiazovivin for the first 24 hrs after
passaging. Cell aggregates (EBs) were allowed to grow for a total
of 16 days with media refreshed every 48 hrs by automated methods.
EBs were imaged before being harvested and lysed using automated
methods and cell lysate analyzed with custom NanoString codesets
(Pluri25 and 3GL (Kahler et al., 2013 on the Nanostring nCounter
system according to manufacturer's instructions.
General Methods
[0427] Pluripotency of iPSCs and hESCs was verified by
immunofluorescence for the markers: Nanog (Cell Signalling
Technology, #4903), Oct4 (#09-0023), Sox2 (#09-0024), SSEA4
(#09-0006), Tra 1-81 (#09-0011), Tra 1-60 (#09-00110; all
Stemgent). Images were acquired using a Celigo, Nikon Eclipse TE
2000-U or Olympus BX41 fluorescent microscopes. Pluripotency was
also analyzed by FACS analysis for CD-13, SSEA4 and Tra 1-60 on an
ARIA-IIu.TM. SOU Cell Sorter as previously described (Kahler et
al., 2013). DNA and RNA were isolated from cells using High Pure
PCR Template Preparation kits (Roche, #11796828001), and RNeasy
Micro kits (Qiagen, #74004) respectively. DNA/RNA was analyzed
using a NanoString nCounter system following using NanoString's
recommended procedures.
Statistical Methods
[0428] Statistical analysis was performed using custom R scripts
(Team, 2014). Pluripotency/differentiation scores of candidate iPSC
lines were quantified by calculating the median t-score (moderate
t-test) of pluripotent/differentiation markers gene expression in
comparison to the distribution of expression values for a reference
set of 15 hESC lines. The previously described Scorecard method
(Bock et al., 2011) was used to measure the differentiation
propensity of day 16 EBs formed from robotically derived iPSCs and
compared against a new reference set of 10 established hESC lines
in order to maintain consistency of culturing conditions. To
quantitate the variance in deriving iPSC lines using different
methods, standard deviation in gene expression for cell lines was
measured and grouped by different derivation methods. The analysis
included all genes that were designated as markers for pluripotent,
endoderm, mesoderm, and ectoderm cell state. To assess the
significance of gene expression variation difference between two
cell line groups, the Wilcoxen signed rank test was used.
Extended Experimental Procedures
Donor Recruitment and Biopsy Collection
[0429] Dermatology patients undergoing a regularly scheduled biopsy
and volunteers from a diverse population were recruited to donate a
biopsy for the generation of induced pluripotent stem cells.
Volunteers free from bleeding disorders and/or prone to excessive
scarring were scheduled to donate a 3 mm punch biopsy at a
collaborating dermatology clinic. Prior to their participation, all
participants provided their written informed consent and study
approval was obtained from Western Institutional Review Board. The
samples were taken from an area of the body to the doctor's
discretion, usually the upper arm or leg. In addition to the
biopsies, health information questionnaires were used to collect
information such as health and medication history, social history
and ethnic background. Upon collection, the samples and
accompanying questionnaires were de-identified using a unique ID
and returned to the NYSCF Human Subjects Research (HSR) staff. The
information provided within the questionnaires was then transferred
by the HSR staff to Redcap, a password protected database, linking
the de-identified data to the anonymous sample ID for the
laboratory researchers and the samples utilized for the generation
of stem cell lines.
Automated Systems Description
[0430] We designed three integrated robotic platforms that fully
automate the iPSC generation and characterization workflow. In
brief, cells are housed in Cytomat incubators and automated method
scripts call out plates onto robotic decks for processing. The
first platform for fibroblast banking consists of a Hamilton
Starlet liquid handler with a plate shuttle directly connecting a
Cytomat C24 incubator. Additional devices such as a Celigo cell
imager, an Agilent Vspin centrifuge, and a Hamilton Decapper were
integrated to facilitate fibroblast growth tracking, passaging and
freezing processes. The second platform for iPSC generation is a
cluster of three independent liquid handling systems connected by a
Hamilton Rack Runner robotic arm and rail. This format allows
parallel processing on multiple systems. Each system has been
customized for its intended purpose with a combination of channel
pipettors, plate heaters, shakers, tilters, and cooling modules.
Usage of shared automated devices such as the Hamilton Rack Runner,
Cytomat C48 incubator, Celigo cell imager, Agilent Vspin, and
Hamilton Decapper are controlled by a reservation system. The third
platform for iPSC characterization and banking is a mirror cluster
with a slightly different device configuration for optimized
96-well plate handling.
[0431] All Hamilton STAR liquid handling systems are contained
within NuAire BSL II biosafety cabinets to maintain a sterile
operating environment during manipulation of cell culture plates.
Remaining components are enclosed in a Hepa filtered hood to
maintain a sterile operating environment during transportation of
cell culture plates between systems and devices.
[0432] Control, scheduling and inventory software integrate with
method scripts for fully automated operation of the systems. Each
method outputs detailed log and mapping files of processing steps,
and Dropcam video monitoring cameras record system activity.
Consumable usage and reagent barcodes are also automatically
tracked on a database.
Automated Biopsy Outgrowth and Fibroblast Cell Culture
[0433] Somatic cell lines (dermal fibroblasts) were derived from
patient tissue samples collected at collaborating clinics in
Complete M106 media which contains Medium 106 (Life Technologies,
#M-106-500), 50.times. Low Serum Growth Supplement (Life
Technologies, #S-003-10) and 100.times. Antibiotic-Antimycotic
(Life Technologies, #154240-062). Samples were de-identified and
assigned an internal barcode for tracking identity and passage
number.
[0434] Each sample was washed 3 times in Biopsy Plating Media and
cleaned with a disposable scalpel and autoclaved forceps to remove
blood, fat and epithelial tissue. Biopsy Plating Media contains
Knockout.TM.-DMEM (Life Technologies #10829-018), 10% FBS (Life
Technologies, #100821-147), 2 mM GlutaMAX (Life Technologies,
#35050-061), 0.1 mM MEM Non-Essential Amino Acids (Life
Technologies, #11140-050), 1.times. Antibiotic-Antimycotic, 0.1 mM
2-Mercaptoethanol (Life Technologies, #21985-023) and 1%
Nucleosides (Millipore, #ES-008-D). Depending on initial tissue
sample size, 2-3 clean 1 mm pieces were transferred to one well of
a 6 well tissue culture plate (Corning, #3516) and allowed to dry
down for 15 minutes. After drying, 3 mL of biopsy plating media
were added dropwise to each well containing tissue pieces and
placed in a quarantine incubator for 10 days to allow for initial
outgrowth undisturbed. Plates were then transferred to an automated
incubator (Cytomat, Thermo Fisher) for routine cell culture on the
automated system. All reagents used for automated methods were
assigned internal barcodes encoding media aliquots and reagent lot
numbers and scanned into individual methods.
[0435] Fibroblasts were maintained in Complete M106 media for one
week and monitored by a Celigo automated imager (Nexcelom) for
outgrowth before being changed into antibiotic free M106 media for
3 days. A 200 uL aliquot of fibroblast cultured media from each
well of a 6 well plate, representing 1 patient sample, was
robotically redistributed into a 96 well v-Bottom plate (Evergreen,
#222-8031) and prepped for mycoplasma testing on system 2. System
2, a separate liquid handling robot was used to perform a
mycoplasma luminescent assay using the MycoAlert Mycoplasma
Detection kit (Lonza, #LT107-318) with the accompanying MycoAlert
Assay Control Set (Lonza, #LT07-518) and read on an integrated
BioTek Synergy HT imaging system.
[0436] Wells that passed mycoplasma detection on system 2 were
enzymatically passaged using TrypLE CTS (Life Technologies,
#A12859-01) into a new 6 well daughter plate, keeping source wells
separate at a 1:1 ratio on system 1. Passaged cells were maintained
robotically in Complete M106 on System 1 and monitored using the
Celigo automated imager for doubling times and ideal freezing
confluence. Upon reaching confluence, each well of the daughter
plate was enzymatically passaged using TrypLE Select CTS, pooled
and resuspended in 1.5 ml of CTS Syntha-a-Freeze (Life
Technologies, #A13717-01). Three 500 uL aliquots of the 1.5 mL
resuspended cell suspension were transferred robotically into three
2D barcoded Matrix tubes (Thermo Scientific, #3741) for
cryopreservation. Matrix tubes, within their rack, were placed in a
CoolBox.TM. 96F System (Biocision, #BCS-147). After 24 hours, one
of three cryopreserved matrix tubes representing one patient
sample, was transferred from the CoolBox system to an automated
-80.degree. C. Sample Access Manager (SAM, Hamilton Storage
Technologies) where samples are inventoried and selected for
reprogramming runs. The sample access manager inventory database
allows for flexible recall and downstream process batching of tubes
for reprogramming based on multiple factors including density,
growth rates and disease group. The remaining two matrix tubes of
the same sample were transferred from the CoolBox system to liquid
nitrogen for long-term storage.
Automated Fibroblast Thawing
[0437] Fibroblasts frozen in matrix tubes, stored within the SAM
were removed in batches of 20 and manually counted to determine
cell number and viability. Cells were manually resuspended into
matrix tubes at known cell numbers, and frozen using the Biocision
CoolBox. At the point of thaw 48 matrix tubes, typically consisting
of duplicates of 20 cell lines and 8 BJ fibroblast controls, were
removed and placed onto System 3. Cells were thawed in a 37.degree.
C. water bath for 30 seconds, before being placed on the robot
deck. Upon starting the method tubes were decapped, fibroblast
growth medium consisting of DMEM (#11965), 10% FBS, Glutamax,
2-Mercaptoethanol (all Life Technologies) was added to each vial,
recapped and automatically centrifuged. The supernatant was
subsequently removed, and the fibroblasts resuspended in fresh
media before being transferred to 4, pre-barcoded, 12 well plates
(Corning, #3513). Mapping files, traced through a centralized
monitoring system, were automatically generated through the use of
user-generated worklists. Cells were automatically transferred, via
the RackRunner, to a cytomat where cells were housed. Each 12 well
plate was fed every three days, with automated imaging occurring at
least three times over a 10 day growth period.
Automated Cell Seeding (12 w to 24 w Passaging)
[0438] In brief, cells grown in 12 well plates were washed and
dissociated with TrypLE Select CTS. Following neutralization with
fibroblast growth medium, 5% (50 .mu.L) of the cell suspension was
transferred into a 96 well BD imaging plate (BD Biosciences,
#353219) pre-filled with 50 .mu.L of PBS (Life Technologies,
#14190-144) containing 5 .mu.g/mL Hoechst 33342 (Sigma, #B2261) and
1 .mu.g/mL Propidium Iodide (Life Technologies, #P3566). The
imaging plate was centrifuged for 2 minutes, before being subjected
to a cell count using the Celigo's Dead/Total application. The cell
counts were auto-exported with the liquid handling software
automatically calculating the exact volume of cell suspension
required for transfer into daughter wells of a 24 well plate
(Corning, #3526). The Dead/Total cell count and confluence readout
were recorded in each method run. Following the passage, cells
remaining the in the original 12 well plate were re-fed and allowed
to re-expand for downstream DNA isolation.
Automated Geltrex.TM. Plate Coating
[0439] For Geltrex.TM. plate coating, 1 mL of Geltrex.TM. was
diluted into 99 mL of pre-chilled DMEM-F12 (Life Technologies,
#10565-018) and kept at 4.degree. C. on a module in System 7.
Pre-chilled plates in either 96 well or 24 well plate formats were
automatically coated with 100 .mu.L or 500 .mu.L of the pre-chilled
Geltrex.TM. solution respectively. Coated plates were sealed and
stored for a maximum for 2 weeks at 4.degree. C. for later use to
avoid premature gelling. Prior to use, plates were incubated at
37.degree. C. for 1 hour.
Automated Reprogramming
[0440] For initial testing with Sendai virus (Life Technologies,
#A1378001), a method was established to allow automated addition of
the Sendai virus to the passaged fibroblasts. Following a medium
exchange into fresh fibroblast growth medium the virus, kept
chilled on a cooling block on system 3, was added dropwise into
each well of the 24 well plate. Cells were briefly shaken for 10
seconds, before being returned to the cytomat incubator via the
RackRunner. Cells were medium exchanged daily and monitored for the
presence of colonies with automated imaging via the Celigo. For
mRNA transfections, an mRNA reprogramming kit (Stemgent, #00-0071)
was used. In brief, 4 hours prior to miRNA transfection the day
after passaging, cells were equilibrated in Pluriton
NUFF-conditioned medium (Stemgent) containing 2500.times.
supplement and 200 ng/ml B18R (both supplied with kits). Following
equilibration, cells were transfected with miRNA on days 0 and 4,
with mRNA transfections occurring on days 1-10. The miRNA/mRNA mix
was robotically added, dropwise, to each well of the 24 well plate
on system 3, followed by a 10 second shaking to disperse the mRNA
mix throughout the well. Each day, prior to transfection, plates
were media exchanged with pre-conditioned Pluriton medium
containing supplement and B18R. After 10 transfections, cells were
fed for a further 5 days with the pre-conditioned Pluriton media
containing the 2500.times. supplement. A transition to Freedom
media (Life Technologies, #A14577SA) was made with 50% medium
exchanges over the subsequent 2 days and cells were further grown
for up to 30 days before being sorted. Since growth of fungi and
mycoplasma can be very slow, and the use of antibiotics can mask
the presence of bacteria in cell cultures. The whole process of
automated somatic cell reprogramming and expansion of the generated
iPSC lines has been processed in antibiotic free media. Strict
policies were implemented on temperature control, and non-reuse of
warmed reagents as well as barcode tracking systems to prevent
variations in media and growth factor quality to control
environmental growth conditions during culture. Strict guidelines
to maintain the sterile conditions of the liquid handling systems
and integrated devices were also implemented.
Automated iPS Cell Sorting
[0441] The automated iPS cell sorting method was based on a
previously developed FACS method (Kahler et al, 2013, PloS one). In
brief, the worklist defined the 24-well source plate to be sorted
and the 96-well destination plates that the sorted iPS cells should
be seeded into. The 24-well plate was called from the Cytomat, and
half of the samples were processed at a time. Cells from 12 wells
were dissociated with Accutase and transferred into half of a
24-deep well harvest plate (E&K Scientific, #EK-2053-S). After
a 2 minute centrifugation step, the supernatant was removed, and
cell pellets were resuspended with FACS buffer. 20 .mu.L of human
anti-fibroblast magnetic beads (Miltenyi Biotec, #130-050-601) was
added to cells, allowed to incubate for 15 minutes, and then washed
with FACS buffer to remove the unbound antibody. Following an
additional centrifugation, cells were resuspended with 500 .mu.L of
FACS buffer and applied to a column block on a magnetic separator
system (MultiMACS.TM. Cell24 Separator Plus, Miltenyi Biotec,
#130-098-637). 500 .mu.L of FACS buffer was then applied (.times.3)
as washes, resulting in un-reprogrammed fibroblasts staying bound
to the column, with reprogrammed cells passing through and
collected as a 2 mL volume in a 24-deep well collection plate. The
collection plate was centrifuged for 2 minutes, supernatant was
removed, and cell pellets were resuspended in 400 .mu.L Freedom
medium supplemented with 1 uM Thiazovivin (Stemgent, #04-0017).
Quadruplicate aliquots of the mixture containing 100 ul of cells
were seeded into 4 wells of a Geltrex pre-coated, 96-well BD black
imaging plate and serially diluted over a 3-fold range. The
automated method looped through again to process the second half of
the 24-well source plate.
Automated Cell Consolidation
[0442] This Example describes an automated method for consolidating
the iPS colonies that passed quality control measures of confluency
readout (>=15%), typical human ESC morphology (e.g. cells with
large nuclei, small amount of cytoplasm, and form compact monolayer
colony) and TRA-1-60 surface marker expression screening (Celigo
Tumorsphere Analysis). Wells in 96-well sorted plates were
identified, and a cherry-picking worklist was created to dictate
source and destination transfer patterns. Per run, pairs of 96-well
source plates were called from the Cytomat and processed together,
until the destination plate was filled. Selected wells were washed
and incubated with 75 .mu.L of 0.05 mM EDTA for 6 minutes.
Automated trituration by tips promoted cell dissociation, and 100
.mu.L of cell mixtures were transferred into a new Geltrex-coated
destination plate. For the first 24 hours, cells were cultured with
Freedom medium supplemented with 1 .mu.M Thiazovivin, after which
cells were fed with Freedom daily. The task of cherry picking cells
from targeted wells was formulated as a combinatorial optimization,
where the goal was to efficiently select target clones with good
recovery and without disturbing cell integrity, according to
confluency read and morphological characteristics captured the day
after consolidation.
Automated iPS Cell Passaging and Expansion
[0443] For cell passage of entire 96-well plates, a worklist was
created, indicating source and destination plates. All
liquid-handling steps herein occurred in the entire plate at once.
The source plate was placed on the deck and cell media was
aspirated. Cells were washed once with Accutase before a further
addition of 25 .mu.L per well. Accutase incubation was for 5
minutes at 37.degree. C. on a heated shaker. Cells were neutralized
with 175 .mu.L Freedom media containing 1 .mu.M thiazovivin, and
transferred to an intermediate 96-well V-bottom plate (Evergreen,
#222-8031-01V). Cells were centrifuged for 5 minutes at 300 RCF
before supernatants were aspirated and cells resuspended in Freedom
media with 1 .mu.M Thiazovivin. Destination plates, previously
robotically coated with Geltrex.TM. and previously robotically
pre-processed by removal of Geltrex.TM. suspension and addition of
Freedom media with 1 .mu.M thiazovivin, were retrieved from a
Cytomat incubator and placed on the deck. Cell suspensions were
transferred from the intermediate plate to the new destination
plate. Destination plates were returned to the Cytomat
incubator.
Automated Cell Freezing (Passage to Cryovials)
[0444] A worklist was created, indicating which 96-well plates were
to be frozen into 2D barcoded Matrix tubes in Matrix racks. All
liquid-handling steps use a 96-head. Media was aspirated and cells
were washed with 50 .mu.L Accutase before a further addition of 50
.mu.L of Accutase was added per well and cells were incubated at
room temperature for 12 minutes. Enzyme neutralization was
performed by the addition of Freedom media containing 1 .mu.M
Thiazovivin. Cell suspensions were transferred to an intermediate
96-well V-bottom plate and centrifuged for 5 minutes at 300 RCF.
The Matrix rack was automatically de-capped and replaced onto the
deck. Supernatants were aspirated and cells were resuspended in 200
.mu.L Synth-a-Freeze. Cell suspensions were transferred to the
Matrix tubes before being re-capped and manually placed into a
CoolBox and stored -80.degree. C. before being transferred 24 hours
later to liquid nitrogen for long term storage.
Automated Cell Thawing (Thawing of Matrix Rack with 96 Matrix
Tubes)
[0445] A Geltrex coated 96 well plate was retrieved from the
Cytomat incubator. Liquid handling steps were performed with a
96-head. Tubes in the Matrix rack were capped and de-capped when
necessary. 700 .mu.L of Freedom media with 1 .mu.M Thiazovivin was
added to each vial. The tubes in the Matrix rack were centrifuged
for 5 minutes at 300 RCF. Supernatant was removed and cells were
resuspended in 125 .mu.L of Freedom media with thiazovivin; 100
.mu.L was transferred to the 96 well plate. The plate was placed in
the Cytomat incubator. A 10 .mu.volume of cell suspension remaining
in each tube was used for Dead/Total cell count by the Celigo
imager.
Automated EB Formation
[0446] Cells were dissociated with Accutase for 5 minutes at
37.degree. C. and plated in suspension into 96 well V-bottom plates
(Greiner, #651161) in the presence of human ES culture media
without bFGF and with 1 .mu.M Thiazovivin using System 7. Human ES
media consists of Knockout.TM.-DMEM (#10829-018), 10% Knockout
Serum Replacement (#10828-028), 1% Glutamax (#35050-079), MEM
nonessential amino acids (#11140-050), 0.1 mM 2-mercaptoethanol
(21985-023); All Life Technologies). Cells from one individual well
were dispensed into 6 daughter wells in a culture volume of 150
.mu.L/well to create 6 total EBs per starting well. After 24 hours,
100 .mu.L of media was removed and added fresh media without
Thiazovivin. Media exchanges were performed every 48 hours. On day
16, the EBs were imaged using a Celigo to determine their presence
prior to collection by the liquid handler workstation. EBs were
lysed through the addition of Lysis buffer using a Bravo Automated
Liquid Handling Platform (Agilent Technologies). Lysis buffer
2.times. contained (0.5% N-Lauroylsarcosine Sodium salt
(Sigma-Aldrich, #61747), 4M Guanidine Thiocyanate (Sigma-Aldrich,
#50983), 200 mM 2-mercaptoethanol (Sigma-Aldrich, #63689), 0.02
Sodium Citrate (Sigma-Aldrich, #C8532), 2% DMSO (Sigma-Aldrich,
#D2650). Cell extracts were quantified with Quant-iT.TM. RNA Assay
Kit (Life Technologies, #Q-33140). Subsequently, 100 ng of cell
extract was used for gene expression analysis on the NanoString
nCounter system following manufacturer's protocol. A custom codeset
was used which covers 98 genes representing early differentiation
markers of the three germ layers (Kahler, D J et al., 2013).
Immunofluorescence Staining
[0447] Cell lines, including hES and hiPS were rinsed twice with
1.times.PBS, fixed with 4% paraformaldehyde (Santa Cruz,
#sc-281692) in PBS for 20 min at room temperature and permeabilized
with PBS containing 0.1% Triton X-100 (herein referred to as PBST;
Sigma-Aldrich, #T8787) for 30 min. Nonspecific binding sites were
blocked by incubation with PBST containing 10% donkey serum
(Jackson Labs, #017-000-1210) for 2 hours at room temperature.
Cells were subsequently incubated overnight at 4.degree. C. in PBST
containing 10% donkey serum and specific primary antibodies: 1:500
anti-Human Oct4 (Stemgent, #09-0023), 1:100 anti-human Nanog (Cell
Signaling Technologies, #4903), 1:500 anti-Human Sox2 (Stemgent,
#09-0024), 1:250 anti-human SSEA4 (Abcam, #ab16287), 1:250
anti-human Tra 1-81 (Stemgent, #09-0010) 1:250 anti-human Tra 1-60
(Stemgent, #09-0010). Following 3 washes in PBS, cells were
incubated with one of the following secondary antibodies: Alexa
Fluor.RTM. 488 donkey anti-Mouse (#A-21202; 1:1000 dilution) and
Alexa Fluor.RTM. 555 donkey anti-rabbit IgG (#A-21428; 1:1000
dilution). After washing twice with 1.times.PBS, the samples were
incubated for 10 min with Hoechst (1 .mu.g/ml) in PBS, followed by
a final wash in PBS. Alkaline phosphatase staining was performed
according to the manufacturer's instructions (SK-5100).
Fluorescence images were captured with the Celigo, Nikon Eclipse TE
2000-U or Olympus BX41 fluorescent microscope.
[0448] To determine pluripotency of automated iPSCs, cells were
stained for CD-13 (BD Biosciences, #555394; 1:100 dilution), SSEA-4
(BD Bioscience, #560219; 1:100 dilution), Tra 1-60 (BD Bioscience,
#560173; 1:100 dilution) and DAPI (Life Technologies)(1:15000
dilution). Stained cells were analyzed on a 5 laser BD Biosciences
ARIA-IIu.TM. SOU Cell Sorter. The resulting data were analyzed
using FlowJo software (Treestar).
DNA Isolation
[0449] DNA was isolated from both iPSCs and fibroblasts. Following
the passage of cells from a 12 well to a 24 well, the fibroblasts
remaining within the 12 well plate were robotically cultured for
10-12 days before being manually passaged to 6 well plates. Upon
reaching .about.90% confluence, as monitored through the Celigo,
each 6-well plate was manually treated with TypLE Select CTS and
the resulting cell pellet collected in a 96 deep well plate
(Corning, #3960). The trough was sealed and frozen at -80.degree.
C. until DNA extraction. iPSCs were robotically passaged from 96
well plates into 24 well plates before being robotically harvested
into 24 well plates and sealed before being stored at -80.degree.
C. DNA isolation from the cell pellets was achieved using the High
Pure Template PCR Template Preparation Kit (Roche, #11796828001) as
per the manufacturer's instructions with the following
modifications: 1) cells were treated with 4 .mu.L of RNase (Qiagen,
#19101) for 2 minutes whilst resuspended in PBS; 2) DNA was eluted
in 30 .mu.L of water.
Cell Line Karyotyping and ID Testing
[0450] Cell lines were karyotyped and an identification record of
each line was made using Nanostring technology. Karyotyping was
undertaken using the Nanostring nCounter Human Karyotype Panel
(Nanostring Technologies, USA) and performed as per the
manufacturer's instructions. In brief, the protocol is as follows:
600 ng of genomic DNA was Alu1 digested at 37.degree. C. for 2
hours, before being denatured at 95.degree. C. for 5 minutes. To
prevent renaturing samples were kept on ice. A total of 300 ng of
Alu1-digested DNA per sample was mixed with hybridization buffer,
capture and reporter codes. Following a 16 hour incubation at
65.degree. C., samples were transferred to a Nanostring Prep
station where hybridized DNA was bound to an imaging cartridge
before imaging. Using reference samples, a copy number was
calculated for each chromosome following normalization of the data
using nSolver (Nanostring Technologies, USA) and Microsoft Excel.
The same protocol was used for a proprietary codeset that allows
the identification of genomic repeat elements. This codeset is
based upon 28 previously identified Copy Number Polymorphic
regions. (Tyson, C. et al. Expansion of a 12-kb VNTR containing the
REXO1L1 gene cluster underlies the microscopically visible
euchromatic variant of 8q21.2. Eur J Hum Genet 22, 458-463 (2014)).
A dissimilarity score between a given pair of samples was
calculated as the sum of squared differences between the samples'
normalized, log-transformed probe values.
[0451] Gene expression analysis was performed using either a custom
nCounter code set for pluripotency (Pluri25) or a custom nCounter
code set for early differentiation markers into all three germ
layers (3GL) previously described in (Kahler. D J et al., 2013).
Cell extract containing 100 ng of RNA per sample, previously
quantified with Quant-iT.TM. RNA Assay Kit (Life Technologies), was
mixed with hybridization buffer, capture and reporter probes.
Following a 16 hour incubation at 65.degree. C., samples were
transferred to a Nanostring Prep station, where hybridized
fluorescently-labeled RNA was bound to an imaging cartridge before
imaging. Data was normalized using nSolver (Nanostring
Technologies, USA). Clustering was performed using the R software.
R Core Team (2013). R: A language and environment for statistical
computing. R Foundation for Statistical Computing, Vienna, Austria.
ISBN 3-900051-07-0.
REFERENCES FOR EXAMPLE 5
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[0484] While several exemplary embodiments of the invention have
been described, the invention is not limited to these embodiments.
Sequence CWU 1
1
24123DNAArtificial SequencePrimer 1ccccagggcc ccattttggt acc
23220DNAArtificial SequencePrimer 2ggcacaaact ccaggttttc
20320DNAArtificial SequencePrimer 3acactgcccc tctcacacat
20422DNAArtificial SequencePrimer 4gggttttctc catgctgttt ct
22522DNAArtificial SequencePrimer 5acccacacag gtgagaaacc tt
22622DNAArtificial SequencePrimer 6gttgggaact tgaccatgat tg
22722DNAArtificial SequencePrimer 7agcagaggag caaaagctca tt
22822DNAArtificial SequencePrimer 8ccaaagtcca atttgaggca gt
22923DNAArtificial SequencePrimer 9ccccagggcc ccattttggt acc
231022DNAArtificial SequencePrimer 10aacctacagg tggggtcttt ca
221120DNAArtificial SequencePrimer 11acactgcccc tctcacacat
201222DNAArtificial SequencePrimer 12aacctacagg tggggtcttt ca
221320DNAArtificial SequencePrimer 13gaccacctcg ccttacacat
201422DNAArtificial SequencePrimer 14aacctacagg tggggtcttt ca
221522DNAArtificial SequencePrimer 15agcagaggag caaaagctca tt
221622DNAArtificial SequencePrimer 16aacctacagg tggggtcttt ca
221719DNAArtificial SequencePrimer 17tagctgtgct cgggctact
191818DNAArtificial SequencePrimer 18tctctgctgg atgacgcg
181920DNAArtificial SequencePrimer 19gagaaggaga agctggagca
202020DNAArtificial SequencePrimer 20gtgaagtgag ggctcccata
202120DNAArtificial SequencePrimer 21agaaccccaa gatgcacaac
202220DNAArtificial SequencePrimer 22tggagtggga ggaagaggta
202320DNAArtificial SequencePrimer 23acctggcgag tctgacatgg
202423DNAArtificial SequencePrimer 24tcttcatgtg taaggcgagg tgg
23
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